=>> Building biology/gkl build started at Wed Mar 18 13:45:18 EDT 2026 port directory: /usr/ports/biology/gkl package name: gkl-0.9.1_1 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p3 FreeBSD 15.0-RELEASE-p3 1500068 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 631 Mar 6 20:23 /usr/ports/biology/gkl/Makefile Ports top last git commit: 8c988f802ea2 Ports top unclean checkout: no Port dir last git commit: 693b58e8e410 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 02 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p3 1500068 UNAME_r=15.0-RELEASE-p3 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_0_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gkl/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gkl/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gkl/work/.cache HOME=/wrkdirs/usr/ports/biology/gkl/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gkl/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gkl/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gkl/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gkl/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gkl/work/.cache HOME=/wrkdirs/usr/ports/biology/gkl/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gkl/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gkl/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- CMAKE_BUILD_TYPE="release" JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gkl" EXAMPLESDIR="share/examples/gkl" DATADIR="share/gkl" WWWDIR="www/gkl" ETCDIR="etc/gkl" --End PLIST_SUB-- --SUB_LIST-- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="8 11" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gkl DOCSDIR=/usr/local/share/doc/gkl EXAMPLESDIR=/usr/local/share/examples/gkl WWWDIR=/usr/local/www/gkl ETCDIR=/usr/local/etc/gkl --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gkl-0.9.1_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> gkl-0.9.1_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gkl-0.9.1_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by gkl-0.9.1_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by gkl-0.9.1_1 for building => SHA256 Checksum OK for Intel-HLS-GKL-0.9.1_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by gkl-0.9.1_1 for building ===> Extracting for gkl-0.9.1_1 => SHA256 Checksum OK for Intel-HLS-GKL-0.9.1_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for gkl-0.9.1_1 ===> Applying FreeBSD patches for gkl-0.9.1_1 from /usr/ports/biology/gkl/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gkl-0.9.1_1 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> gkl-0.9.1_1 depends on executable: gmake - found ===> Returning to build of gkl-0.9.1_1 ===> gkl-0.9.1_1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.10_1.pkg [pkg.DaveG.ca] Installing cmake-core-3.31.10_1... [pkg.DaveG.ca] `-- Installing expat-2.7.4... [pkg.DaveG.ca] `-- Extracting expat-2.7.4: .......... done [pkg.DaveG.ca] `-- Installing jsoncpp-1.9.6_1... [pkg.DaveG.ca] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg.DaveG.ca] `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | `-- Installing libunistring-1.4.2... [pkg.DaveG.ca] | `-- Extracting libunistring-1.4.2: .......... done [pkg.DaveG.ca] `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] `-- Installing libuv-1.52.0... [pkg.DaveG.ca] `-- Extracting libuv-1.52.0: .......... done [pkg.DaveG.ca] `-- Installing rhash-1.4.6... [pkg.DaveG.ca] `-- Extracting rhash-1.4.6: .......... done [pkg.DaveG.ca] Extracting cmake-core-3.31.10_1: .......... done ===> gkl-0.9.1_1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of gkl-0.9.1_1 ===> gkl-0.9.1_1 depends on file: /usr/local/openjdk8/bin/java - not found ===> Installing existing package /packages/All/openjdk8-8.482.08.1.pkg [pkg.DaveG.ca] Installing openjdk8-8.482.08.1... [pkg.DaveG.ca] `-- Installing alsa-lib-1.2.15.3... [pkg.DaveG.ca] `-- Extracting alsa-lib-1.2.15.3: .......... done [pkg.DaveG.ca] `-- Installing dejavu-2.37_4... [pkg.DaveG.ca] | `-- Installing fontconfig-2.17.1,1... [pkg.DaveG.ca] | | `-- Installing freetype2-2.14.1... [pkg.DaveG.ca] | | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | | `-- Installing png-1.6.55... [pkg.DaveG.ca] | | `-- Extracting png-1.6.55: .......... done [pkg.DaveG.ca] | | `-- Extracting freetype2-2.14.1: .......... done [pkg.DaveG.ca] | `-- Extracting fontconfig-2.17.1,1: .......... done [pkg.DaveG.ca] | `-- Installing mkfontscale-1.2.3... [pkg.DaveG.ca] | | `-- Installing libfontenc-1.1.9... [pkg.DaveG.ca] | | `-- Extracting libfontenc-1.1.9: ...... done [pkg.DaveG.ca] | `-- Extracting mkfontscale-1.2.3: .... done [pkg.DaveG.ca] `-- Extracting dejavu-2.37_4: .......... done [pkg.DaveG.ca] `-- Installing giflib-5.2.2... [pkg.DaveG.ca] `-- Extracting giflib-5.2.2: .......... done [pkg.DaveG.ca] `-- Installing java-zoneinfo-2021.e... [pkg.DaveG.ca] `-- Extracting java-zoneinfo-2021.e: .......... done [pkg.DaveG.ca] `-- Installing javavmwrapper-2.7.10_1... [pkg.DaveG.ca] `-- Extracting javavmwrapper-2.7.10_1: .......... done [pkg.DaveG.ca] `-- Installing libX11-1.8.13,1... [pkg.DaveG.ca] | `-- Installing libxcb-1.17.0... [pkg.DaveG.ca] | | `-- Installing libXau-1.0.12... [pkg.DaveG.ca] | | `-- Extracting libXau-1.0.12: .......... done [pkg.DaveG.ca] | | `-- Installing libXdmcp-1.1.5... [pkg.DaveG.ca] | | `-- Installing xorgproto-2024.1... [pkg.DaveG.ca] | | `-- Extracting xorgproto-2024.1: .......... done [pkg.DaveG.ca] | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg.DaveG.ca] | `-- Extracting libxcb-1.17.0: .......... done [pkg.DaveG.ca] `-- Extracting libX11-1.8.13,1: .......... done [pkg.DaveG.ca] `-- Installing libXext-1.3.6,1... [pkg.DaveG.ca] `-- Extracting libXext-1.3.6,1: .......... done [pkg.DaveG.ca] `-- Installing libXi-1.8.2,1... [pkg.DaveG.ca] | `-- Installing libXfixes-6.0.1... [pkg.DaveG.ca] | `-- Extracting libXfixes-6.0.1: ....... done [pkg.DaveG.ca] `-- Extracting libXi-1.8.2,1: .......... done [pkg.DaveG.ca] `-- Installing libXrender-0.9.12... [pkg.DaveG.ca] `-- Extracting libXrender-0.9.12: ....... done [pkg.DaveG.ca] `-- Installing libXt-1.3.0,1... [pkg.DaveG.ca] | `-- Installing libICE-1.1.2,1... [pkg.DaveG.ca] | `-- Extracting libICE-1.1.2,1: .......... done [pkg.DaveG.ca] | `-- Installing libSM-1.2.6,1... [pkg.DaveG.ca] | `-- Extracting libSM-1.2.6,1: ........ done [pkg.DaveG.ca] `-- Extracting libXt-1.3.0,1: .......... done [pkg.DaveG.ca] `-- Installing libXtst-1.2.5... [pkg.DaveG.ca] `-- Extracting libXtst-1.2.5: .......... done [pkg.DaveG.ca] `-- Installing libinotify-20240724_3... [pkg.DaveG.ca] `-- Extracting libinotify-20240724_3: .......... done [pkg.DaveG.ca] Extracting openjdk8-8.482.08.1: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ===== Message from freetype2-2.14.1: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===== Message from libinotify-20240724_3: -- You might want to consider increasing the kern.maxfiles tunable if you plan to use this library for applications that need to monitor activity of a lot of files. ===== Message from openjdk8-8.482.08.1: -- This OpenJDK implementation may require procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: proc /proc procfs rw 0 0 ===> gkl-0.9.1_1 depends on file: /usr/local/openjdk8/bin/java - found ===> Returning to build of gkl-0.9.1_1 ===> gkl-0.9.1_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> gkl-0.9.1_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of gkl-0.9.1_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gkl-0.9.1_1 depends on shared library: libisal.so - not found ===> Installing existing package /packages/All/isa-l-2.31.1.pkg [pkg.DaveG.ca] Installing isa-l-2.31.1... [pkg.DaveG.ca] Extracting isa-l-2.31.1: .......... done ===> gkl-0.9.1_1 depends on shared library: libisal.so - found (/usr/local/lib/libisal.so) ===> Returning to build of gkl-0.9.1_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for gkl-0.9.1_1 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/gkl/work/.build CMake Warning (dev) at CMakeLists.txt:1 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is Clang 19.1.7 -- The CXX compiler identification is Clang 19.1.7 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Found Java: /usr/local/bin/java (found suitable version "1.8.0.482", minimum required is "1.8") -- Found JNI: /usr/local/openjdk8/include found components: AWT JVM -- Found OpenMP_C: -fopenmp=libomp (found version "5.1") -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.1") -- Found OpenMP: TRUE (found version "5.1") -- Configuring done (2.8s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_C_FLAGS_RELEASE CMAKE_EXE_LINKER_FLAGS CMAKE_MODULE_LINKER_FLAGS FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/gkl/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for gkl-0.9.1_1 /usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1 -B/wrkdirs/usr/ports/biology/gkl/work/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/gkl/work/.build/CMakeFiles /wrkdirs/usr/ports/biology/gkl/work/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- --- src/main/native/utils/CMakeFiles/gkl_utils.dir/all --- --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/all --- --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- /usr/bin/make -f src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/build.make src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/depend --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /usr/bin/make -f src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/build.make src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/depend --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /usr/bin/make -f src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/build.make src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/depend --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/all --- /usr/bin/make -f src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/build.make src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/depend --- src/main/native/utils/CMakeFiles/gkl_utils.dir/all --- /usr/bin/make -f src/main/native/utils/CMakeFiles/gkl_utils.dir/build.make src/main/native/utils/CMakeFiles/gkl_utils.dir/depend --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- /usr/bin/make -f src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/build.make src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/depend --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/depend --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/depend --- --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/all --- --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/depend --- --- src/main/native/utils/CMakeFiles/gkl_utils.dir/all --- --- src/main/native/utils/CMakeFiles/gkl_utils.dir/depend --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/depend --- --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/depend --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1 /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm /wrkdirs/usr/ports/biology/gkl/work/.build /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/DependInfo.cmake --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1 /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression /wrkdirs/usr/ports/biology/gkl/work/.build /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/DependInfo.cmake --- 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-std=gnu++11 -fPIC -fopenmp=libomp -mavx -mavx2 -mavx512f -mavx512dq -mavx512vl -mavx512bw -MD -MT src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/avx512_impl.cc.o -MF CMakeFiles/gkl_pdhmm.dir/avx512_impl.cc.o.d -o CMakeFiles/gkl_pdhmm.dir/avx512_impl.cc.o -c /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx512_impl.cc --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/all --- --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/IntelSmithWaterman.cc.o --- [ 52%] Building CXX object src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/IntelSmithWaterman.cc.o --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/avx_impl.cc.o --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm && /usr/local/libexec/ccache/c++ -Dgkl_pairhmm_omp_EXPORTS -I/usr/local/openjdk8/include -I/usr/local/openjdk8/include/freebsd -I/wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FORTIFY_SOURCE=2 -O3 -Wformat -Werror=format-security -Wconversion -Wfloat-conversion -Wbool-compare -fstack-protector-all -fno-strict-overflow -fno-delete-null-pointer-checks -fwrapv -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++11 -fPIC -fopenmp=libomp -mavx -MD -MT src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/avx_impl.cc.o -MF CMakeFiles/gkl_pairhmm_omp.dir/avx_impl.cc.o.d -o CMakeFiles/gkl_pairhmm_omp.dir/avx_impl.cc.o -c /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx_impl.cc --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression && /usr/local/bin/cmake -Dcfgdir= -P 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src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/avx512_impl.cc.o -MF CMakeFiles/gkl_pairhmm.dir/avx512_impl.cc.o.d -o CMakeFiles/gkl_pairhmm.dir/avx512_impl.cc.o -c /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/avx_impl.cc.o --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm && /usr/local/libexec/ccache/c++ -Dgkl_pairhmm_EXPORTS -I/usr/local/openjdk8/include -I/usr/local/openjdk8/include/freebsd -I/wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FORTIFY_SOURCE=2 -O3 -Wformat -Werror=format-security -Wconversion -Wfloat-conversion -Wbool-compare -fstack-protector-all -fno-strict-overflow -fno-delete-null-pointer-checks -fwrapv -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++11 -fPIC -mavx -MD -MT src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/avx_impl.cc.o -MF CMakeFiles/gkl_pairhmm.dir/avx_impl.cc.o.d -o CMakeFiles/gkl_pairhmm.dir/avx_impl.cc.o -c /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx_impl.cc --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/avx512_impl.cc.o --- [ 55%] Building CXX object src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/avx512_impl.cc.o --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/all --- --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/smithwaterman_common.cc.o --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/smithwaterman && /usr/local/libexec/ccache/c++ -Dgkl_smithwaterman_EXPORTS -I/usr/local/openjdk8/include -I/usr/local/openjdk8/include/freebsd -I/wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FORTIFY_SOURCE=2 -O3 -Wformat -Werror=format-security -Wconversion -Wfloat-conversion -Wbool-compare -fstack-protector-all -fno-strict-overflow -fno-delete-null-pointer-checks -fwrapv -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/smithwaterman_common.cc.o -MF CMakeFiles/gkl_smithwaterman.dir/smithwaterman_common.cc.o.d -o CMakeFiles/gkl_smithwaterman.dir/smithwaterman_common.cc.o -c /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/smithwaterman_common.cc --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/IntelSmithWaterman.cc.o --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/smithwaterman && /usr/local/libexec/ccache/c++ -Dgkl_smithwaterman_EXPORTS -I/usr/local/openjdk8/include -I/usr/local/openjdk8/include/freebsd -I/wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FORTIFY_SOURCE=2 -O3 -Wformat -Werror=format-security -Wconversion -Wfloat-conversion -Wbool-compare -fstack-protector-all -fno-strict-overflow -fno-delete-null-pointer-checks -fwrapv -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/IntelSmithWaterman.cc.o -MF CMakeFiles/gkl_smithwaterman.dir/IntelSmithWaterman.cc.o.d -o CMakeFiles/gkl_smithwaterman.dir/IntelSmithWaterman.cc.o -c /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/IntelSmithWaterman.cc --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm && /usr/local/libexec/ccache/c++ -Dgkl_pairhmm_omp_EXPORTS -I/usr/local/openjdk8/include -I/usr/local/openjdk8/include/freebsd -I/wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FORTIFY_SOURCE=2 -O3 -Wformat -Werror=format-security -Wconversion -Wfloat-conversion -Wbool-compare -fstack-protector-all -fno-strict-overflow -fno-delete-null-pointer-checks -fwrapv -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++11 -fPIC -fopenmp=libomp -mavx -mavx2 -mavx512f -mavx512dq -mavx512vl -MD -MT src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/avx512_impl.cc.o -MF CMakeFiles/gkl_pairhmm_omp.dir/avx512_impl.cc.o.d -o CMakeFiles/gkl_pairhmm_omp.dir/avx512_impl.cc.o -c /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/pairhmm_common.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] 1 warning generated. --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-mkdir --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/pairhmm_common.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] 1 warning generated. --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/all --- --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/avx2_impl.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx2_impl.cc:26: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx2-smithwaterman.h:30: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:88:36: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 88 | int32_t hwidth = D_MAX_SEQ_LEN + AVX_LENGTH; | ~~~~~~ ~~~~~~~~~~~~~~^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:89:36: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 89 | int32_t ewidth = D_MAX_SEQ_LEN + AVX_LENGTH; | ~~~~~~ ~~~~~~~~~~~~~~^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:91:28: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 91 | int32_t *E = E_ + tid * 6 * (D_MAX_SEQ_LEN + AVX_LENGTH); | ~~~~^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:108:37: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 108 | seq1Rev[D_MAX_SEQ_LEN - 1 - i] = p->seq1[i]; | ~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:151:45: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 151 | int32_t diagInd = D_MAX_SEQ_LEN + diag; | ~~~~~~~ ~~~~~~~~~~~~~~^~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:151:47: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 151 | int32_t diagInd = D_MAX_SEQ_LEN + diag; | ~ ^~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:152:42: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 152 | int32_t inde = D_MAX_SEQ_LEN - i; | ~~~~ ~~~~~~~~~~~~~~^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:152:44: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 152 | int32_t inde = D_MAX_SEQ_LEN - i; | ~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:164:45: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 164 | int32_t diagInd = D_MAX_SEQ_LEN + diag; | ~~~~~~~ ~~~~~~~~~~~~~~^~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:164:47: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 164 | int32_t diagInd = D_MAX_SEQ_LEN + diag; | ~ ^~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:165:42: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 165 | int32_t inde = D_MAX_SEQ_LEN - i; | ~~~~ ~~~~~~~~~~~~~~^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:165:44: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 165 | int32_t inde = D_MAX_SEQ_LEN - i; | ~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:178:36: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 178 | VEC_STREAM(backTrack + antiDiag * D_MAX_SEQ_LEN + backTrackInd, bt_vec); | ^~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx2-functions.h:61:37: note: expanded from macro 'VEC_STREAM' 61 | _mm256_stream_si256((__m256i *)(__addr), __v) | ^~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx2_impl.cc:26: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx2-smithwaterman.h:30: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:190:45: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 190 | int32_t diagInd = D_MAX_SEQ_LEN + diag; | ~~~~~~~ ~~~~~~~~~~~~~~^~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:190:47: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 190 | int32_t diagInd = D_MAX_SEQ_LEN + diag; | ~ ^~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:191:42: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 191 | int32_t inde = D_MAX_SEQ_LEN - i; | ~~~~ ~~~~~~~~~~~~~~^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:191:44: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 191 | int32_t inde = D_MAX_SEQ_LEN - i; | ~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:204:36: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 204 | VEC_STREAM(backTrack + antiDiag * D_MAX_SEQ_LEN + backTrackInd, bt_vec); | ^~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx2-functions.h:61:37: note: expanded from macro 'VEC_STREAM' 61 | _mm256_stream_si256((__m256i *)(__addr), __v) | ^~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx2_impl.cc:26: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx2-smithwaterman.h:30: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:213:49: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 213 | H[cur + ((D_MAX_SEQ_LEN + 2 * jhi - antiDiag) >> 1)] = open + (jhi - 1) * extend; | ~ ^~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:213:41: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 213 | H[cur + ((D_MAX_SEQ_LEN + 2 * jhi - antiDiag) >> 1)] = open + (jhi - 1) * extend; | ~ ~~^~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:213:15: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 213 | H[cur + ((D_MAX_SEQ_LEN + 2 * jhi - antiDiag) >> 1)] = open + (jhi - 1) * extend; | ^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:214:49: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 214 | H[cur + ((D_MAX_SEQ_LEN + 2 * jlo - antiDiag) >> 1)] = open + (ilo - 1) * extend; | ~ ^~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:214:41: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 214 | H[cur + ((D_MAX_SEQ_LEN + 2 * jlo - antiDiag) >> 1)] = open + (ilo - 1) * extend; | ~ ~~^~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:214:15: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 214 | H[cur + ((D_MAX_SEQ_LEN + 2 * jlo - antiDiag) >> 1)] = open + (ilo - 1) * extend; | ^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:218:49: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 218 | H[cur + ((D_MAX_SEQ_LEN + 2 * jhi - antiDiag) >> 1)] = 0; | ~ ^~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:218:41: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 218 | H[cur + ((D_MAX_SEQ_LEN + 2 * jhi - antiDiag) >> 1)] = 0; | ~ ~~^~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:218:15: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 218 | H[cur + ((D_MAX_SEQ_LEN + 2 * jhi - antiDiag) >> 1)] = 0; | ^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:219:49: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 219 | H[cur + ((D_MAX_SEQ_LEN + 2 * jlo - antiDiag) >> 1)] = 0; | ~ ^~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:219:41: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 219 | H[cur + ((D_MAX_SEQ_LEN + 2 * jlo - antiDiag) >> 1)] = 0; | ~ ~~^~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:219:15: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 219 | H[cur + ((D_MAX_SEQ_LEN + 2 * jlo - antiDiag) >> 1)] = 0; | ^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:222:27: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 222 | E[D_MAX_SEQ_LEN - ilo] = lowInitValue; | ~ ^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:227:70: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 227 | int32_t score = H[cur + ((D_MAX_SEQ_LEN + jlo + 1 - (ilo - 1)) >> 1)]; | ~ ~~~~^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:227:55: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 227 | int32_t score = H[cur + ((D_MAX_SEQ_LEN + jlo + 1 - (ilo - 1)) >> 1)]; | ~ ^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:227:31: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 227 | int32_t score = H[cur + ((D_MAX_SEQ_LEN + jlo + 1 - (ilo - 1)) >> 1)]; | ^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:241:70: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 241 | int32_t score = H[cur + ((D_MAX_SEQ_LEN + jhi - 1 - (ihi + 1)) >> 1)]; | ~ ~~~~^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:241:55: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 241 | int32_t score = H[cur + ((D_MAX_SEQ_LEN + jhi - 1 - (ihi + 1)) >> 1)]; | ~ ^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:241:31: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 241 | int32_t score = H[cur + ((D_MAX_SEQ_LEN + jhi - 1 - (ihi + 1)) >> 1)]; | ^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:254:53: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 254 | p->score = H[cur + ((D_MAX_SEQ_LEN + ncol - nrow) >> 1)]; | ~ ^~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:254:46: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 254 | p->score = H[cur + ((D_MAX_SEQ_LEN + ncol - nrow) >> 1)]; | ~ ^~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:254:22: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 254 | p->score = H[cur + ((D_MAX_SEQ_LEN + ncol - nrow) >> 1)]; | ^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:309:51: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 309 | btrInd = antiDiag * D_MAX_SEQ_LEN + j - 1; | ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:309:49: warning: implicit conversion changes signedness: 'int16_t' (aka 'short') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 309 | btrInd = antiDiag * D_MAX_SEQ_LEN + j - 1; | ~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:309:22: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 309 | btrInd = antiDiag * D_MAX_SEQ_LEN + j - 1; | ^~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:314:57: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 314 | btrInd = antiDiag * D_MAX_SEQ_LEN + j - jLo - 1; | ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:314:53: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 314 | btrInd = antiDiag * D_MAX_SEQ_LEN + j - jLo - 1; | ~ ^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:314:49: warning: implicit conversion changes signedness: 'int16_t' (aka 'short') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 314 | btrInd = antiDiag * D_MAX_SEQ_LEN + j - jLo - 1; | ~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:314:22: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 314 | btrInd = antiDiag * D_MAX_SEQ_LEN + j - jLo - 1; | ^~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:449:49: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] 449 | p->cigarCount = (uint32_t)strnlen(p->cigar, curSize); | ~~~~~~~ ^~~~~~~ 49 warnings generated. --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/smithwaterman_common.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] 1 warning generated. --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/MathUtils.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/MathUtils.cc:64:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 64 | double *result = (double *)_mm_malloc((to - from) * sizeof(double), 64); | ~~~^~~~~~ ~ 2 warnings generated. --- src/main/native/utils/CMakeFiles/gkl_utils.dir/all --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/utils/utils.cc:39: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/utils/../common/avx.h:154:42: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 152 | uint32_t avx512_skx_mask = (1 << 16) | // AVX-512F | ~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ 153 | (1 << 17) | // AVX-512DQ | ~~~~~~~~~~~~~~~~~~~~~~~~ 154 | (1 << 30) | // AVX-512BW | ~~~~~~~~~~^~~~~~~~~~~~~~ 155 | (1 << 31); // AVX-512VL | ~~~~~~~~~ 2 warnings generated. --- src/main/native/utils/libgkl_utils.so --- --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- --- src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-download --- --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/avx512_impl.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx512-pdhmm.h:28: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/MathUtils-avx.h:79:45: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned long' [-Wsign-conversion] 79 | double *elements = (double *)_mm_malloc(size * sizeof(double), 64); | ^~~~ ~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx512-pdhmm.h:30: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:46:52: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 46 | size_t sizeOfTables = paddedMaxHaplotypeLength * SIMD_WIDTH_DOUBLE * sizeof(double); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:883:72: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 883 | INT_TYPE *read_ins_qual_vec = (INT_TYPE *)_mm_malloc(maxReadLength * SIMD_WIDTH_DOUBLE * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:884:72: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 884 | INT_TYPE *read_del_qual_vec = (INT_TYPE *)_mm_malloc(maxReadLength * SIMD_WIDTH_DOUBLE * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:885:62: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 885 | INT_TYPE *gcp_vec = (INT_TYPE *)_mm_malloc(maxReadLength * SIMD_WIDTH_DOUBLE * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:960:73: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 960 | INT_TYPE *hap_bases_vec = (INT_TYPE *)_mm_malloc(maxHaplotypeLength * SIMD_WIDTH_DOUBLE * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:961:65: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 961 | hap_pdbases_vec = (INT_TYPE *)_mm_malloc(maxHaplotypeLength * SIMD_WIDTH_DOUBLE * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:962:69: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 962 | INT_TYPE *read_bases_vec = (INT_TYPE *)_mm_malloc(maxReadLength * SIMD_WIDTH_DOUBLE * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:963:68: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 963 | INT_TYPE *read_qual_vec = (INT_TYPE *)_mm_malloc(maxReadLength * SIMD_WIDTH_DOUBLE * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:1194:52: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'unsigned long' [-Wsign-conversion] 1194 | g_constantsAreInitialized = (bool *)_mm_malloc(totalThreads * sizeof(bool), ALIGN_SIZE); | ^~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:1195:40: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'unsigned long' [-Wsign-conversion] 1195 | g_initialized = (bool *)_mm_malloc(totalThreads * sizeof(bool), ALIGN_SIZE); | ^~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:1196:73: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 1196 | g_prev_hap_bases_lengths = (INT_TYPE *)_mm_malloc(SIMD_WIDTH_DOUBLE * totalThreads * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:1197:45: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'unsigned long' [-Wsign-conversion] 1197 | int32_t *status = (int32_t *)_mm_malloc(totalThreads * sizeof(int32_t), ALIGN_SIZE); | ^~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:1251:9: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32] 1251 | for (int32_t i = 0; i < roundedBatchSize; i += SIMD_WIDTH_DOUBLE) | ^~~ 15 warnings generated. --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/avx2_impl.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx2_impl.cc:26: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx2-pdhmm.h:28: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/MathUtils-avx.h:79:45: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned long' [-Wsign-conversion] 79 | double *elements = (double *)_mm_malloc(size * sizeof(double), 64); | ^~~~ ~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx2_impl.cc:26: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx2-pdhmm.h:29: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:46:52: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 46 | size_t sizeOfTables = paddedMaxHaplotypeLength * SIMD_WIDTH_DOUBLE * sizeof(double); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:219:27: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 219 | VEC_MASK_TYPE mask1 = VEC_CMP_NE_INT(temp, zeroVec); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx2-functions.h:229:62: note: expanded from macro 'VEC_CMP_NE_INT' 229 | VEC_AND_NOT_INT(VEC_CMP_EQ_INT(__v1, __v2), VEC_SET1_INT(0xFFFFFFFF)) | ~~~~~~~~~~~~~^~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx2-functions.h:197:20: note: expanded from macro 'VEC_SET1_INT' 197 | _mm_set1_epi32(__v1) | ~~~~~~~~~~~~~~ ^~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx2-functions.h:107:28: note: expanded from macro 'VEC_AND_NOT_INT' 107 | _mm_andnot_si128(__v1, __v2) | ^~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx2_impl.cc:26: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx2-pdhmm.h:29: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:222:27: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 222 | VEC_MASK_TYPE mask2 = VEC_CMP_NE_INT(temp, zeroVec); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx2-functions.h:229:62: note: expanded from macro 'VEC_CMP_NE_INT' 229 | VEC_AND_NOT_INT(VEC_CMP_EQ_INT(__v1, __v2), VEC_SET1_INT(0xFFFFFFFF)) | ~~~~~~~~~~~~~^~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx2-functions.h:197:20: note: expanded from macro 'VEC_SET1_INT' 197 | _mm_set1_epi32(__v1) | ~~~~~~~~~~~~~~ ^~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx2-functions.h:107:28: note: expanded from macro 'VEC_AND_NOT_INT' 107 | _mm_andnot_si128(__v1, __v2) | ^~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx2_impl.cc:26: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/avx2-pdhmm.h:29: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:883:72: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 883 | INT_TYPE *read_ins_qual_vec = (INT_TYPE *)_mm_malloc(maxReadLength * SIMD_WIDTH_DOUBLE * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:884:72: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 884 | INT_TYPE *read_del_qual_vec = (INT_TYPE *)_mm_malloc(maxReadLength * SIMD_WIDTH_DOUBLE * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:885:62: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 885 | INT_TYPE *gcp_vec = (INT_TYPE *)_mm_malloc(maxReadLength * SIMD_WIDTH_DOUBLE * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:960:73: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 960 | INT_TYPE *hap_bases_vec = (INT_TYPE *)_mm_malloc(maxHaplotypeLength * SIMD_WIDTH_DOUBLE * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:961:65: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 961 | hap_pdbases_vec = (INT_TYPE *)_mm_malloc(maxHaplotypeLength * SIMD_WIDTH_DOUBLE * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:962:69: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 962 | INT_TYPE *read_bases_vec = (INT_TYPE *)_mm_malloc(maxReadLength * SIMD_WIDTH_DOUBLE * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:963:68: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 963 | INT_TYPE *read_qual_vec = (INT_TYPE *)_mm_malloc(maxReadLength * SIMD_WIDTH_DOUBLE * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:1142:58: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned long' [-Wsign-conversion] 1142 | INT_TYPE *hap_bases_lengths = (INT_TYPE *)_mm_malloc(batchSize * sizeof(INT_TYPE), ALIGN_SIZE); | ^~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:1143:59: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned long' [-Wsign-conversion] 1143 | INT_TYPE *read_bases_lengths = (INT_TYPE *)_mm_malloc(batchSize * sizeof(INT_TYPE), ALIGN_SIZE); | ^~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:1194:52: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'unsigned long' [-Wsign-conversion] 1194 | g_constantsAreInitialized = (bool *)_mm_malloc(totalThreads * sizeof(bool), ALIGN_SIZE); | ^~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:1195:40: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'unsigned long' [-Wsign-conversion] 1195 | g_initialized = (bool *)_mm_malloc(totalThreads * sizeof(bool), ALIGN_SIZE); | ^~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:1196:73: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 1196 | g_prev_hap_bases_lengths = (INT_TYPE *)_mm_malloc(SIMD_WIDTH_DOUBLE * totalThreads * sizeof(INT_TYPE), ALIGN_SIZE); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm.h:1197:45: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'unsigned long' [-Wsign-conversion] 1197 | int32_t *status = (int32_t *)_mm_malloc(totalThreads * sizeof(int32_t), ALIGN_SIZE); | ^~~~~~~~~~~~ ~ 18 warnings generated. --- src/main/native/utils/CMakeFiles/gkl_utils.dir/all --- [ 58%] Linking CXX shared library libgkl_utils.so --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/avx512_impl.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:176: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:165: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:154: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:143: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:132: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:121: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:110: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:99: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:88: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:77: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:66: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:55: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:44: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:33: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:22: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:176: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:165: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:154: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:143: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:132: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:121: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:110: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:99: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:88: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:77: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:66: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:55: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:44: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:33: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:22: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:35: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:24: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:41: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~~~~~ ^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:21: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; | ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:38: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; | ~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:95:5: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 95 | VEC_BLENDV(distmChosen, distm, _1_distm, bitMaskVec.getCombinedMask()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:136:25: note: expanded from macro 'VEC_BLENDV' 136 | _512_INT_TYPE val = VEC_SET1_VAL_32(); \ | ^~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:171:23: note: expanded from macro 'VEC_SET1_VAL_32' 171 | _mm512_set1_epi32(0x80000000) | ~~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:35: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:177:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 177 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:178:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 178 | UNION_TYPE packed3; packed3.d = VEC_SET1_VAL(3.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:201:13: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 201 | M_t_1_y = M_t_1; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:216:11: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 216 | M_t_y = M_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:17: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:22: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:29: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:36: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:41: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:48: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:55: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:60: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:67: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:74: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:81: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:21: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:264:14: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 264 | HAP_TYPE hap; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:270:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 270 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ --- src/main/native/utils/CMakeFiles/gkl_utils.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/utils && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gkl_utils.dir/link.txt --verbose=1 --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:367:20: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 367 | UNION_TYPE sumMX; | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:136: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:117: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:98: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:79: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:60: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:41: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:22: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:136: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:117: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:98: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/avx512_impl.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:176: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/pdhmm-serial.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm-serial.cc:529:9: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long') to 'int' [-Wshorten-64-to-32] 529 | for (int32_t i = 0; i < testcase; i++) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm-serial.cc:610:9: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long') to 'int' [-Wshorten-64-to-32] 610 | for (int32_t i = 0; i < testcase; i++) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:79: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:165: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/pdhmm-serial.cc:729:9: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long') to 'int' [-Wshorten-64-to-32] 729 | for (int32_t i = 0; i < testcase; i++) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4 warnings generated. --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/IntelPDHMM.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/IntelPDHMM.cc:31: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:84:52: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 84 | int64_t memoryPerPair = (maxReadLength * 5 + maxHaplotypeLength * 2) * sizeof(int8_t) + sizeof(double) + 2 * sizeof(int64_t); --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:60: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:154: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:114:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 114 | delete[] nativeReadBases[i]; | ~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:115:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 115 | delete[] nativeReadQuals[i]; | ~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:116:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 116 | delete[] nativeInsertionGop[i]; | ~~~~~~~~~~~~~~~~~~ ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:41: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:143: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:117:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 117 | delete[] nativeDeletionGop[i]; | ~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:118:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 118 | delete[] nativeOverallGcp[i]; | ~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:123:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 123 | delete[] nativeHapBases[i]; | ~~~~~~~~~~~~~~ ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:22: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:39: --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:132: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:124:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 124 | delete[] nativeHapPDBases[i]; | ~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:194:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 194 | int8_t *readBases = nativeReadBases[currReadIndex]; | ~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:195:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 195 | int8_t *readQuals = nativeReadQuals[currReadIndex]; | ~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:24: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:41: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~~~~~ ^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:21: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:121: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:196:55: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 196 | int8_t *insertionGop = nativeInsertionGop[currReadIndex]; | ~~~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:197:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 197 | int8_t *deletionGop = nativeDeletionGop[currReadIndex]; | ~~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:198:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 198 | int8_t *overallGcp = nativeOverallGcp[currReadIndex]; --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- | ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:38: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; | ~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:95:5: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 95 | VEC_BLENDV(distmChosen, distm, _1_distm, bitMaskVec.getCombinedMask()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:136:25: note: expanded from macro 'VEC_BLENDV' 136 | _512_INT_TYPE val = VEC_SET1_VAL_32(); \ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:110: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:199:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 199 | int readLength = nativeReadLengths[currReadIndex]; | ~~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:203:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 203 | int8_t *hapBases = nativeHapBases[currHaplotypeIndex]; | ~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:204:55: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- | ^~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:171:24: note: expanded from macro 'VEC_SET1_VAL_32' 171 | _mm512_set1_epi64(0x8000000000000000) | ~~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:39: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:177:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 177 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:99: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- 204 | int8_t *hapPDBases = nativeHapPDBases[currHaplotypeIndex]; | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:205:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 205 | int haplotypeLength = nativeHapLengths[currHaplotypeIndex]; | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:304:57: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 304 | batchReadBases = (int8_t *)_mm_malloc(batchSize * maxReadLength * sizeof(int8_t), ALIGN_SIZE); | ~~~~~~~~~~^~~~~~~~~~~~~~~ ~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:178:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 178 | UNION_TYPE packed3; packed3.d = VEC_SET1_VAL(3.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:201:13: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 201 | M_t_1_y = M_t_1; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:216:11: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 216 | M_t_y = M_t; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:88: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:305:57: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 305 | batchReadQuals = (int8_t *)_mm_malloc(batchSize * maxReadLength * sizeof(int8_t), ALIGN_SIZE); | ~~~~~~~~~~^~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:306:60: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 306 | batchInsertionGop = (int8_t *)_mm_malloc(batchSize * maxReadLength * sizeof(int8_t), ALIGN_SIZE); | ~~~~~~~~~~^~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:307:59: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:17: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:22: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:29: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:77: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- 307 | batchDeletionGop = (int8_t *)_mm_malloc(batchSize * maxReadLength * sizeof(int8_t), ALIGN_SIZE); | ~~~~~~~~~~^~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:308:58: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 308 | batchOverallGcp = (int8_t *)_mm_malloc(batchSize * maxReadLength * sizeof(int8_t), ALIGN_SIZE); | ~~~~~~~~~~^~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:309:56: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 309 | batchHapBases = (int8_t *)_mm_malloc(batchSize * maxHaplotypeLength * sizeof(int8_t), ALIGN_SIZE); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ ~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:36: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:41: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:66: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:310:58: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 310 | batchHapPDBases = (int8_t *)_mm_malloc(batchSize * maxHaplotypeLength * sizeof(int8_t), ALIGN_SIZE); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:311:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 311 | batchResult = (double *)_mm_malloc(batchSize * sizeof(double), ALIGN_SIZE); | ^~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:312:49: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 312 | batchHapLengths = (int64_t *)_mm_malloc(batchSize * sizeof(int64_t), ALIGN_SIZE); --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:48: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:55: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:55: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- | ^~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:313:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] 313 | batchReadLengths = (int64_t *)_mm_malloc(batchSize * sizeof(int64_t), ALIGN_SIZE); | ^~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:334:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 334 | nativeReadBases.resize(totalReads); | ~~~~~~ ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:335:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 335 | nativeReadQuals.resize(totalReads); | ~~~~~~ ^~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:60: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:67: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:44: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:336:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 336 | nativeInsertionGop.resize(totalReads); | ~~~~~~ ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:337:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 337 | nativeDeletionGop.resize(totalReads); | ~~~~~~ ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:338:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 338 | nativeOverallGcp.resize(totalReads); | ~~~~~~ ^~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:74: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:81: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:33: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:339:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 339 | nativeReadLengths.resize(totalReads); | ~~~~~~ ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:356:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 356 | nativeReadBases[i] = new int8_t[readBasesLength]; | ~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:357:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 357 | nativeReadQuals[i] = new int8_t[readQualsLength]; | ~~~~~~~~~~~~~~~ ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:21: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:270:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 270 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:22: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:358:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 358 | nativeInsertionGop[i] = new int8_t[insertionGopLength]; | ~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:359:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 359 | nativeDeletionGop[i] = new int8_t[deletionGopLength]; | ~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:360:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 360 | nativeOverallGcp[i] = new int8_t[overallGcpLength]; | ~~~~~~~~~~~~~~~~ ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:176: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:362:89: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 362 | env->GetByteArrayRegion(readBasesArray, 0, readBasesLength, nativeReadBases[i]); | ~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:363:89: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 363 | env->GetByteArrayRegion(readQualsArray, 0, readQualsLength, nativeReadQuals[i]); | ~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:364:98: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:165: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- 364 | env->GetByteArrayRegion(insertionGopArray, 0, insertionGopLength, nativeInsertionGop[i]); | ~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:365:95: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 365 | env->GetByteArrayRegion(deletionGopArray, 0, deletionGopLength, nativeDeletionGop[i]); | ~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:366:92: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 366 | env->GetByteArrayRegion(overallGcpArray, 0, overallGcpLength, nativeOverallGcp[i]); --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:154: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- | ~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:368:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 368 | nativeReadLengths[i] = readBasesLength; | ~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:378:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 378 | nativeHapBases.resize(totalHaplotypes); | ~~~~~~ ^~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:379:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 379 | nativeHapPDBases.resize(totalHaplotypes); | ~~~~~~ ^~~~~~~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:143: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:380:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 380 | nativeHapLengths.resize(totalHaplotypes); | ~~~~~~ ^~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:391:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 391 | nativeHapBases[i] = new int8_t[haplotypeBasesLength]; | ~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:392:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 392 | nativeHapPDBases[i] = new int8_t[haplotypePDBasesLength]; | ~~~~~~~~~~~~~~~~ ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:132: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:394:98: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 394 | env->GetByteArrayRegion(haplotypeBasesArray, 0, haplotypeBasesLength, nativeHapBases[i]); | ~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:395:104: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 395 | env->GetByteArrayRegion(haplotypePDBasesArray, 0, haplotypePDBasesLength, nativeHapPDBases[i]); | ~~~~~~~~~~~~~~~~ ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:121: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/JavaData.h:397:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 397 | nativeHapLengths[i] = haplotypeBasesLength; | ~~~~~~~~~~~~~~~~ ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/IntelPDHMM.cc:35: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/../common/avx.h:154:42: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 152 | uint32_t avx512_skx_mask = (1 << 16) | // AVX-512F | ~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ 153 | (1 << 17) | // AVX-512DQ | ~~~~~~~~~~~~~~~~~~~~~~~~ 154 | (1 << 30) | // AVX-512BW | ~~~~~~~~~~^~~~~~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:110: note: expanded from macro 'VEC_SET2' --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- 155 | (1 << 31); // AVX-512VL | ~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm/IntelPDHMM.cc:195:43: warning: implicit conversion changes signedness: 'jint' (aka 'int') to 'unsigned long' [-Wsign-conversion] 195 | double *result = (double *)_mm_malloc(testcase * sizeof(double), ALIGN_SIZE); | ^~~~~~~~ ~ 55 warnings generated. --- src/main/native/pdhmm/libgkl_pdhmm.so --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:99: note: expanded from macro 'VEC_SET2' --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:88: note: expanded from macro 'VEC_SET2' --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:77: note: expanded from macro 'VEC_SET2' --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:66: note: expanded from macro 'VEC_SET2' --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:55: note: expanded from macro 'VEC_SET2' --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:44: note: expanded from macro 'VEC_SET2' --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:367:20: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 367 | UNION_TYPE sumMX; | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:33: note: expanded from macro 'VEC_SET2' --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:35: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:17: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:30:43: note: in instantiation of function template specialization 'compute_full_prob_avx512s' requested here 30 | float (*compute_fp_avx512s)(testcase*) = &compute_full_prob_avx512s; | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:34: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:177:22: note: expanded from macro 'VEC_SET2' --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:35: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:22: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:29: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi32(0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:35: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:24: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:41: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:36: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:41: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~~~~~ ^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:21: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; | ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:38: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; | ~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:48: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:55: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:95:5: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] 95 | VEC_BLENDV(distmChosen, distm, _1_distm, bitMaskVec.getCombinedMask()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:136:25: note: expanded from macro 'VEC_BLENDV' 136 | _512_INT_TYPE val = VEC_SET1_VAL_32(); \ | ^~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-float.h:171:23: note: expanded from macro 'VEC_SET1_VAL_32' 171 | _mm512_set1_epi32(0x80000000) | ~~~~~~~~~~~~~~~~~ ^~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- [ 61%] Performing download step (DIR copy) for 'otc_zlibExternal' --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:60: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:67: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:35: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:177:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 177 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:178:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 178 | UNION_TYPE packed3; packed3.d = VEC_SET1_VAL(3.0); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:74: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:81: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:201:13: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 201 | M_t_1_y = M_t_1; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:216:11: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 216 | M_t_y = M_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:17: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:21: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:264:14: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 264 | HAP_TYPE hap; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:22: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:29: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:270:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 270 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:36: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:41: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:48: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:55: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:60: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:67: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:74: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:81: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:21: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:264:14: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 264 | HAP_TYPE hap; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:270:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 270 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:367:20: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 367 | UNION_TYPE sumMX; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:177:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 177 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:294:9: note: in instantiation of function template specialization 'stripeINITIALIZATIONavx512s' requested here --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 294 | CONCAT(CONCAT(stripeINITIALIZATION,SIMD_ENGINE), PRECISION)(i, ctx, tc, pGAPM, pMM, pMX, pXX, pMY, pYY, rs.d, rsN, distm, _1_distm, distm1D, N_packed256, p_MM , p_GAPM , | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/pairhmm_common.h:37:21: note: expanded from macro 'CONCAT' 37 | #define CONCAT(X,Y) CAT(X,Y) | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/pairhmm_common.h:36:18: note: expanded from macro 'CAT' 36 | #define CAT(X,Y) X##Y | ^ :131:1: note: expanded from here 131 | stripeINITIALIZATIONavx512s | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:30:43: note: in instantiation of function template specialization 'compute_full_prob_avx512s' requested here 30 | float (*compute_fp_avx512s)(testcase*) = &compute_full_prob_avx512s; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:35: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:178:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 178 | UNION_TYPE packed3; packed3.d = VEC_SET1_VAL(3.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:201:13: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 201 | M_t_1_y = M_t_1; | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:39: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:17: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:31:44: note: in instantiation of function template specialization 'compute_full_prob_avx512d' requested here 31 | double (*compute_fp_avx512d)(testcase*) = &compute_full_prob_avx512d; | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:39: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:22: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:29: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:36: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:41: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:367:20: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 367 | UNION_TYPE sumMX; | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:48: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:55: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:136: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:60: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:67: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:117: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:74: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:81: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:98: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:21: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:270:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 270 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:79: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:60: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:41: note: expanded from macro 'VEC_SET2' --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:38:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 38 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:22: note: expanded from macro 'VEC_SET2' --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:136: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:117: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:98: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:79: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:60: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:41: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:38: --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-vector-shift.h:51:11: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 51 | idx = VEC_SET2(); | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:177:22: note: expanded from macro 'VEC_SET2' 177 | _mm512_set_epi64(0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0xFFFFFFFFFFFFFFFF,0x0) | ~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:39: --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:24: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:41: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~~~~~ ^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:21: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- | ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:38: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; | ~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:95:5: warning: implicit conversion changes signedness: 'unsigned long' to 'long long' [-Wsign-conversion] 95 | VEC_BLENDV(distmChosen, distm, _1_distm, bitMaskVec.getCombinedMask()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:136:25: note: expanded from macro 'VEC_BLENDV' 136 | _512_INT_TYPE val = VEC_SET1_VAL_32(); \ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/IntelPairHmm.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- | ^~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-functions-double.h:171:24: note: expanded from macro 'VEC_SET1_VAL_32' 171 | _mm512_set1_epi64(0x8000000000000000) | ~~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:39: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:177:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/avx_impl.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:33: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common/avx.h:154:42: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 152 | uint32_t avx512_skx_mask = (1 << 16) | // AVX-512F | ~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ 153 | (1 << 17) | // AVX-512DQ | ~~~~~~~~~~~~~~~~~~~~~~~~ 154 | (1 << 30) | // AVX-512BW | ~~~~~~~~~~^~~~~~~~~~~~~~ 155 | (1 << 31); // AVX-512VL | ~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:42: --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx_impl.cc:25: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm.h:35: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:24: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:41: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~~~~~ ^~~~~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/JavaData.h:96:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 96 | tc.hap = haplotypes[h]; | ~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/JavaData.h:97:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 97 | tc.haplen = haplotypeLengths[h]; | ~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/JavaData.h:120:75: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 120 | m_env->ReleaseByteArrayElements(m_byteArrays[i].first, m_byteArrays[i].second, 0); | ~~~~~~~~~~~~ ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:21: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; | ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:38: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; | ~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx_impl.cc:25: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm.h:39: --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/JavaData.h:120:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 120 | m_env->ReleaseByteArrayElements(m_byteArrays[i].first, m_byteArrays[i].second, 0); | ~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/JavaData.h:123:81: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 123 | m_env->ReleaseDoubleArrayElements(m_doubleArrays[i].first, m_doubleArrays[i].second, 0); | ~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/JavaData.h:123:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:24: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:41: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~~~~~ ^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:21: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 123 | m_env->ReleaseDoubleArrayElements(m_doubleArrays[i].first, m_doubleArrays[i].second, 0); | ~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:160:93: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 160 | float result_float = g_use_double ? 0.0f : g_compute_full_prob_float(&testcases[i]); | ~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:163:76: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 163 | double result_double = g_compute_full_prob_double(&testcases[i]); | ~~~~~~~~~ ^ 10 warnings generated. --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- | ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:38: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; | ~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~ 9 warnings generated. --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/IntelPairHmm.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:33: --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/avx512_impl.cc.o --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common/avx.h:154:42: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 152 | uint32_t avx512_skx_mask = (1 << 16) | // AVX-512F | ~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ 153 | (1 << 17) | // AVX-512DQ | ~~~~~~~~~~~~~~~~~~~~~~~~ 154 | (1 << 30) | // AVX-512BW | ~~~~~~~~~~^~~~~~~~~~~~~~ 155 | (1 << 31); // AVX-512VL | ~~~~~~~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/avx512_impl.cc.o --- 177 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:367:20: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:178:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 178 | UNION_TYPE packed3; packed3.d = VEC_SET1_VAL(3.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:201:13: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 201 | M_t_1_y = M_t_1; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:216:11: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 216 | M_t_y = M_t; --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/IntelPairHmm.cc.o --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- 367 | UNION_TYPE sumMX; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:177:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 177 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:294:9: note: in instantiation of function template specialization 'stripeINITIALIZATIONavx512d' requested here 294 | CONCAT(CONCAT(stripeINITIALIZATION,SIMD_ENGINE), PRECISION)(i, ctx, tc, pGAPM, pMM, pMX, pXX, pMY, pYY, rs.d, rsN, distm, _1_distm, distm1D, N_packed256, p_MM , p_GAPM , | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/pairhmm_common.h:37:21: note: expanded from macro 'CONCAT' 37 | #define CONCAT(X,Y) CAT(X,Y) | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:42: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/JavaData.h:96:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 96 | tc.hap = haplotypes[h]; | ~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/JavaData.h:97:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 97 | tc.haplen = haplotypeLengths[h]; | ~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/JavaData.h:120:75: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 120 | m_env->ReleaseByteArrayElements(m_byteArrays[i].first, m_byteArrays[i].second, 0); --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/pairhmm_common.h:36:18: note: expanded from macro 'CAT' 36 | #define CAT(X,Y) X##Y | ^ :187:1: note: expanded from here 187 | stripeINITIALIZATIONavx512d | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:31:44: note: in instantiation of function template specialization 'compute_full_prob_avx512d' requested here 31 | double (*compute_fp_avx512d)(testcase*) = &compute_full_prob_avx512d; | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:39: --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/avx512_impl.cc.o --- | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:17: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:22: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/IntelPairHmm.cc.o --- | ~~~~~~~~~~~~ ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:178:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 178 | UNION_TYPE packed3; packed3.d = VEC_SET1_VAL(3.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:201:13: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 201 | M_t_1_y = M_t_1; | ^ 243 warnings generated. --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/JavaData.h:120:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 120 | m_env->ReleaseByteArrayElements(m_byteArrays[i].first, m_byteArrays[i].second, 0); | ~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/JavaData.h:123:81: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 123 | m_env->ReleaseDoubleArrayElements(m_doubleArrays[i].first, m_doubleArrays[i].second, 0); | ~~~~~~~~~~~~~~ ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/avx512_impl.cc.o --- --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src && /usr/local/bin/cmake -E rm -rf /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:29: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:36: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/IntelPairHmm.cc.o --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/JavaData.h:123:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 123 | m_env->ReleaseDoubleArrayElements(m_doubleArrays[i].first, m_doubleArrays[i].second, 0); | ~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:160:93: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] 160 | float result_float = g_use_double ? 0.0f : g_compute_full_prob_float(&testcases[i]); | ~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:163:76: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/avx512_impl.cc.o --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:41: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:48: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/IntelPairHmm.cc.o --- 163 | double result_double = g_compute_full_prob_double(&testcases[i]); | ~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:157:9: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] 157 | for (int i = 0; i < testcases.size(); i++) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 11 warnings generated. --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/avx512_impl.cc.o --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:55: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:60: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:67: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:74: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:81: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:21: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:270:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 270 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:367:20: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 367 | UNION_TYPE sumMX; | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:35: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:17: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:30:43: note: in instantiation of function template specialization 'compute_full_prob_avx512s' requested here 30 | float (*compute_fp_avx512s)(testcase*) = &compute_full_prob_avx512s; | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:35: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:22: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:29: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:36: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:41: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:48: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:55: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:60: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:67: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:74: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:81: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:21: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:264:14: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 264 | HAP_TYPE hap; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:270:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 270 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:367:20: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 367 | UNION_TYPE sumMX; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:177:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 177 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:294:9: note: in instantiation of function template specialization 'stripeINITIALIZATIONavx512s' requested here 294 | CONCAT(CONCAT(stripeINITIALIZATION,SIMD_ENGINE), PRECISION)(i, ctx, tc, pGAPM, pMM, pMX, pXX, pMY, pYY, rs.d, rsN, distm, _1_distm, distm1D, N_packed256, p_MM , p_GAPM , | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/pairhmm_common.h:37:21: note: expanded from macro 'CONCAT' 37 | #define CONCAT(X,Y) CAT(X,Y) | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/pairhmm_common.h:36:18: note: expanded from macro 'CAT' 36 | #define CAT(X,Y) X##Y | ^ :131:1: note: expanded from here 131 | stripeINITIALIZATIONavx512s | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:30:43: note: in instantiation of function template specialization 'compute_full_prob_avx512s' requested here 30 | float (*compute_fp_avx512s)(testcase*) = &compute_full_prob_avx512s; | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:35: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:178:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_F512' may result in an unaligned pointer access [-Walign-mismatch] 178 | UNION_TYPE packed3; packed3.d = VEC_SET1_VAL(3.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:201:13: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 201 | M_t_1_y = M_t_1; | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:39: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:17: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:31:44: note: in instantiation of function template specialization 'compute_full_prob_avx512d' requested here 31 | double (*compute_fp_avx512d)(testcase*) = &compute_full_prob_avx512d; | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:39: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:22: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:29: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:36: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:41: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:48: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:55: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:60: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:67: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:74: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:255:81: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 255 | UNION_TYPE M_t, M_t_1, M_t_2, X_t, X_t_1, X_t_2, Y_t, Y_t_1, Y_t_2, M_t_y, M_t_1_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:263:21: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 263 | UNION_TYPE rs , rsN; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:270:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 270 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:310:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 310 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:319:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 319 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:320:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 320 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:89: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:96: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:103: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:110: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:117: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:124: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:351:133: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 351 | CONCAT(CONCAT(computeMXY,SIMD_ENGINE), PRECISION)(M_t, X_t, Y_t, M_t_y, M_t_2, X_t_2, Y_t_2, M_t_1, X_t_1, M_t_1_y, Y_t_1, | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:51: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:362:66: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 362 | M_t_2 = M_t_1; M_t_1 = M_t; X_t_2 = X_t_1; X_t_1 = X_t; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:23: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:38: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:363:53: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 363 | Y_t_2 = Y_t_1; Y_t_1 = Y_t; M_t_1_y = M_t_y; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:367:20: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 367 | UNION_TYPE sumMX; | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:177:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 177 | UNION_TYPE packed1; packed1.d = VEC_SET1_VAL(1.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:294:9: note: in instantiation of function template specialization 'stripeINITIALIZATIONavx512d' requested here 294 | CONCAT(CONCAT(stripeINITIALIZATION,SIMD_ENGINE), PRECISION)(i, ctx, tc, pGAPM, pMM, pMX, pXX, pMY, pYY, rs.d, rsN, distm, _1_distm, distm1D, N_packed256, p_MM , p_GAPM , | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/pairhmm_common.h:37:21: note: expanded from macro 'CONCAT' 37 | #define CONCAT(X,Y) CAT(X,Y) | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/pairhmm_common.h:36:18: note: expanded from macro 'CAT' 36 | #define CAT(X,Y) X##Y | ^ :187:1: note: expanded from here 187 | stripeINITIALIZATIONavx512d | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:31:44: note: in instantiation of function template specialization 'compute_full_prob_avx512d' requested here 31 | double (*compute_fp_avx512d)(testcase*) = &compute_full_prob_avx512d; | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx512-pairhmm.h:39: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:178:16: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'mix_D512' may result in an unaligned pointer access [-Walign-mismatch] 178 | UNION_TYPE packed3; packed3.d = VEC_SET1_VAL(3.0); | ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:201:13: warning: passing 32-byte aligned argument to 64-byte aligned parameter 'this' of 'operator=' may result in an unaligned pointer access [-Walign-mismatch] 201 | M_t_1_y = M_t_1; | ^ 243 warnings generated. --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- [ 64%] Linking CXX shared library libgkl_pdhmm.so cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pdhmm && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gkl_pdhmm.dir/link.txt --verbose=1 --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/avx_impl.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx_impl.cc:25: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm.h:35: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:24: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:41: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~~~~~ ^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:21: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; | ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:38: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; | ~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx_impl.cc:25: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm.h:39: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:24: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:42:41: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] 42 | char hapChar = ConvertChar::get(tc.hap[col-1]); | ~~~~~~~~~~~ ^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:21: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; | ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/avx-pairhmm-template.h:63:38: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion] 63 | rsArr[ri] = ConvertChar::get(tc.rs[ri+beginRowIndex-1]) ; | ~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~ 9 warnings generated. --- src/main/native/pairhmm/libgkl_pairhmm.so --- --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src && /usr/local/bin/cmake -E copy_directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/otc_zlib /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- [ 67%] Linking CXX shared library libgkl_pairhmm.so cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gkl_pairhmm.dir/link.txt --verbose=1 --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-download --- src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-update --- [ 70%] No update step for 'otc_zlibExternal' cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression && /usr/local/bin/cmake -E echo_append cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-update --- src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-patch --- [ 73%] Performing patch step for 'otc_zlibExternal' cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal && patch < /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/otc_zlib.patch Hmm... Looks like a new-style context diff to me... The text leading up to this was: -------------------------- |*** configure 2023-05-18 15:55:05.049975110 -0800 |--- configure_new 2023-05-18 15:53:58.853492011 -0800 -------------------------- Patching file configure using Plan A... Hunk #1 succeeded at 194. done cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-patch --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- c++: warning: argument unused during compilation: '-static-libstdc++' [-Wunused-command-line-argument] c++: warning: argument unused during compilation: '-static-libgcc' [-Wunused-command-line-argument] --- src/main/native/utils/CMakeFiles/gkl_utils.dir/all --- c++: warning: argument unused during compilation: '-static-libstdc++' [-Wunused-command-line-argument] c++: warning: argument unused during compilation: '-static-libgcc' [-Wunused-command-line-argument] --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- --- src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-configure --- [ 76%] Performing configure step for 'otc_zlibExternal' cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-build && /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/configure --static --prefix=/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- c++: warning: argument unused during compilation: '-static-libstdc++' [-Wunused-command-line-argument] c++: warning: argument unused during compilation: '-static-libgcc' [-Wunused-command-line-argument] --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/all --- --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/avx512_impl.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx512-smithwaterman.h:30: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:88:36: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 88 | int32_t hwidth = D_MAX_SEQ_LEN + AVX_LENGTH; | ~~~~~~ ~~~~~~~~~~~~~~^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:89:36: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 89 | int32_t ewidth = D_MAX_SEQ_LEN + AVX_LENGTH; | ~~~~~~ ~~~~~~~~~~~~~~^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:91:28: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 91 | int32_t *E = E_ + tid * 6 * (D_MAX_SEQ_LEN + AVX_LENGTH); | ~~~~^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:108:37: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 108 | seq1Rev[D_MAX_SEQ_LEN - 1 - i] = p->seq1[i]; | ~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:151:45: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 151 | int32_t diagInd = D_MAX_SEQ_LEN + diag; | ~~~~~~~ ~~~~~~~~~~~~~~^~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:151:47: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 151 | int32_t diagInd = D_MAX_SEQ_LEN + diag; | ~ ^~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:152:42: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 152 | int32_t inde = D_MAX_SEQ_LEN - i; | ~~~~ ~~~~~~~~~~~~~~^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:152:44: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 152 | int32_t inde = D_MAX_SEQ_LEN - i; | ~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:164:45: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 164 | int32_t diagInd = D_MAX_SEQ_LEN + diag; | ~~~~~~~ ~~~~~~~~~~~~~~^~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:164:47: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 164 | int32_t diagInd = D_MAX_SEQ_LEN + diag; | ~ ^~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:165:42: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 165 | int32_t inde = D_MAX_SEQ_LEN - i; | ~~~~ ~~~~~~~~~~~~~~^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:165:44: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 165 | int32_t inde = D_MAX_SEQ_LEN - i; | ~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:178:36: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 178 | VEC_STREAM(backTrack + antiDiag * D_MAX_SEQ_LEN + backTrackInd, bt_vec); | ^~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx512-functions.h:61:37: note: expanded from macro 'VEC_STREAM' 61 | _mm512_stream_si512((__m512i *)(__addr), __v) | ^~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx512-smithwaterman.h:30: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:190:45: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 190 | int32_t diagInd = D_MAX_SEQ_LEN + diag; | ~~~~~~~ ~~~~~~~~~~~~~~^~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:190:47: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 190 | int32_t diagInd = D_MAX_SEQ_LEN + diag; | ~ ^~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:191:42: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 191 | int32_t inde = D_MAX_SEQ_LEN - i; | ~~~~ ~~~~~~~~~~~~~~^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:191:44: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 191 | int32_t inde = D_MAX_SEQ_LEN - i; | ~ ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- --- src/main/native/pairhmm/libgkl_pairhmm_omp.so --- --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/all --- /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:204:36: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 204 | VEC_STREAM(backTrack + antiDiag * D_MAX_SEQ_LEN + backTrackInd, bt_vec); | ^~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx512-functions.h:61:37: note: expanded from macro 'VEC_STREAM' 61 | _mm512_stream_si512((__m512i *)(__addr), __v) | ^~~~~~ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx512_impl.cc:28: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/avx512-smithwaterman.h:30: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:213:49: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 213 | H[cur + ((D_MAX_SEQ_LEN + 2 * jhi - antiDiag) >> 1)] = open + (jhi - 1) * extend; | ~ ^~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:213:41: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 213 | H[cur + ((D_MAX_SEQ_LEN + 2 * jhi - antiDiag) >> 1)] = open + (jhi - 1) * extend; | ~ ~~^~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:213:15: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 213 | H[cur + ((D_MAX_SEQ_LEN + 2 * jhi - antiDiag) >> 1)] = open + (jhi - 1) * extend; | ^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:214:49: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 214 | H[cur + ((D_MAX_SEQ_LEN + 2 * jlo - antiDiag) >> 1)] = open + (ilo - 1) * extend; | ~ ^~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:214:41: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 214 | H[cur + ((D_MAX_SEQ_LEN + 2 * jlo - antiDiag) >> 1)] = open + (ilo - 1) * extend; | ~ ~~^~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:214:15: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 214 | H[cur + ((D_MAX_SEQ_LEN + 2 * jlo - antiDiag) >> 1)] = open + (ilo - 1) * extend; | ^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:218:49: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 218 | H[cur + ((D_MAX_SEQ_LEN + 2 * jhi - antiDiag) >> 1)] = 0; | ~ ^~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:218:41: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 218 | H[cur + ((D_MAX_SEQ_LEN + 2 * jhi - antiDiag) >> 1)] = 0; | ~ ~~^~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:218:15: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 218 | H[cur + ((D_MAX_SEQ_LEN + 2 * jhi - antiDiag) >> 1)] = 0; | ^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:219:49: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 219 | H[cur + ((D_MAX_SEQ_LEN + 2 * jlo - antiDiag) >> 1)] = 0; | ~ ^~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:219:41: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 219 | H[cur + ((D_MAX_SEQ_LEN + 2 * jlo - antiDiag) >> 1)] = 0; | ~ ~~^~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:219:15: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 219 | H[cur + ((D_MAX_SEQ_LEN + 2 * jlo - antiDiag) >> 1)] = 0; | ^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:222:27: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 222 | E[D_MAX_SEQ_LEN - ilo] = lowInitValue; | ~ ^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:227:70: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 227 | int32_t score = H[cur + ((D_MAX_SEQ_LEN + jlo + 1 - (ilo - 1)) >> 1)]; | ~ ~~~~^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:227:55: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 227 | int32_t score = H[cur + ((D_MAX_SEQ_LEN + jlo + 1 - (ilo - 1)) >> 1)]; | ~ ^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:227:31: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 227 | int32_t score = H[cur + ((D_MAX_SEQ_LEN + jlo + 1 - (ilo - 1)) >> 1)]; | ^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:241:70: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 241 | int32_t score = H[cur + ((D_MAX_SEQ_LEN + jhi - 1 - (ihi + 1)) >> 1)]; | ~ ~~~~^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:241:55: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 241 | int32_t score = H[cur + ((D_MAX_SEQ_LEN + jhi - 1 - (ihi + 1)) >> 1)]; | ~ ^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:241:31: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 241 | int32_t score = H[cur + ((D_MAX_SEQ_LEN + jhi - 1 - (ihi + 1)) >> 1)]; | ^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:254:53: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 254 | p->score = H[cur + ((D_MAX_SEQ_LEN + ncol - nrow) >> 1)]; | ~ ^~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:254:46: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 254 | p->score = H[cur + ((D_MAX_SEQ_LEN + ncol - nrow) >> 1)]; | ~ ^~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:254:22: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 254 | p->score = H[cur + ((D_MAX_SEQ_LEN + ncol - nrow) >> 1)]; | ^~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:309:51: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 309 | btrInd = antiDiag * D_MAX_SEQ_LEN + j - 1; | ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:309:49: warning: implicit conversion changes signedness: 'int16_t' (aka 'short') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 309 | btrInd = antiDiag * D_MAX_SEQ_LEN + j - 1; | ~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:309:22: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 309 | btrInd = antiDiag * D_MAX_SEQ_LEN + j - 1; | ^~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:314:57: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion] 314 | btrInd = antiDiag * D_MAX_SEQ_LEN + j - jLo - 1; | ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:314:53: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 314 | btrInd = antiDiag * D_MAX_SEQ_LEN + j - jLo - 1; | ~ ^~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:314:49: warning: implicit conversion changes signedness: 'int16_t' (aka 'short') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 314 | btrInd = antiDiag * D_MAX_SEQ_LEN + j - jLo - 1; | ~ ^ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:314:22: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 314 | btrInd = antiDiag * D_MAX_SEQ_LEN + j - jLo - 1; | ^~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/PairWiseSW.h:449:49: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] 449 | p->cigarCount = (uint32_t)strnlen(p->cigar, curSize); | ~~~~~~~ ^~~~~~~ 49 warnings generated. --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/IntelSmithWaterman.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/IntelSmithWaterman.cc:26: /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman/../common/avx.h:154:42: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 152 | uint32_t avx512_skx_mask = (1 << 16) | // AVX-512F | ~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ 153 | (1 << 17) | // AVX-512DQ | ~~~~~~~~~~~~~~~~~~~~~~~~ 154 | (1 << 30) | // AVX-512BW | ~~~~~~~~~~^~~~~~~~~~~~~~ 155 | (1 << 31); // AVX-512VL | ~~~~~~~~~ 2 warnings generated. --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- [ 79%] Linking CXX shared library libgkl_pairhmm_omp.so --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/all --- --- src/main/native/smithwaterman/libgkl_smithwaterman.so --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gkl_pairhmm_omp.dir/link.txt --verbose=1 c++: warning: argument unused during compilation: '-static-libstdc++' [-Wunused-command-line-argument] c++: warning: argument unused during compilation: '-static-libgcc' [-Wunused-command-line-argument] --- src/main/native/utils/CMakeFiles/gkl_utils.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FORTIFY_SOURCE=2 -O3 -Wformat -Werror=format-security -Wconversion -Wfloat-conversion -Wbool-compare -fstack-protector-all -fno-strict-overflow -fno-delete-null-pointer-checks -fwrapv -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -Xlinker --dependency-file=CMakeFiles/gkl_utils.dir/link.d -static-libstdc++ -static-libgcc -Wl,-z,now -shared -Wl,-soname,libgkl_utils.so -o libgkl_utils.so CMakeFiles/gkl_utils.dir/utils.cc.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib: -fopenmp=libomp --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/all --- [ 82%] Linking CXX shared library libgkl_smithwaterman.so cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/smithwaterman && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gkl_smithwaterman.dir/link.txt --verbose=1 --- src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FORTIFY_SOURCE=2 -O3 -Wformat -Werror=format-security -Wconversion -Wfloat-conversion -Wbool-compare -fstack-protector-all -fno-strict-overflow -fno-delete-null-pointer-checks -fwrapv -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -Xlinker --dependency-file=CMakeFiles/gkl_pdhmm.dir/link.d -static-libstdc++ -static-libgcc -Wl,-z,now -Wl,--no-as-needed -shared -Wl,-soname,libgkl_pdhmm.so -o libgkl_pdhmm.so CMakeFiles/gkl_pdhmm.dir/IntelPDHMM.cc.o CMakeFiles/gkl_pdhmm.dir/avx2_impl.cc.o CMakeFiles/gkl_pdhmm.dir/avx512_impl.cc.o CMakeFiles/gkl_pdhmm.dir/MathUtils.cc.o "CMakeFiles/gkl_pdhmm.dir/pdhmm-serial.cc.o" -L/usr/local/lib -Wl,-rpath,/usr/local/lib: -fopenmp=libomp [ 82%] Built target gkl_pdhmm --- src/main/native/utils/CMakeFiles/gkl_utils.dir/all --- [ 82%] Built target gkl_utils --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FORTIFY_SOURCE=2 -O3 -Wformat -Werror=format-security -Wconversion -Wfloat-conversion -Wbool-compare -fstack-protector-all -fno-strict-overflow -fno-delete-null-pointer-checks -fwrapv -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -Xlinker --dependency-file=CMakeFiles/gkl_pairhmm.dir/link.d -static-libstdc++ -static-libgcc -Wl,-z,now -Wl,--no-as-needed -shared -Wl,-soname,libgkl_pairhmm.so -o libgkl_pairhmm.so CMakeFiles/gkl_pairhmm.dir/IntelPairHmm.cc.o CMakeFiles/gkl_pairhmm.dir/avx_impl.cc.o CMakeFiles/gkl_pairhmm.dir/avx512_impl.cc.o CMakeFiles/gkl_pairhmm.dir/pairhmm_common.cc.o -L/usr/local/lib -Wl,-rpath,:::::::::::::: [ 82%] Built target gkl_pairhmm --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/all --- c++: warning: argument unused during compilation: '-static-libstdc++' [-Wunused-command-line-argument] c++: warning: argument unused during compilation: '-static-libgcc' [-Wunused-command-line-argument] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FORTIFY_SOURCE=2 -O3 -Wformat -Werror=format-security -Wconversion -Wfloat-conversion -Wbool-compare -fstack-protector-all -fno-strict-overflow -fno-delete-null-pointer-checks -fwrapv -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -Xlinker --dependency-file=CMakeFiles/gkl_pairhmm_omp.dir/link.d -static-libstdc++ -static-libgcc -Wl,-z,now -Wl,--no-as-needed -shared -Wl,-soname,libgkl_pairhmm_omp.so -o libgkl_pairhmm_omp.so CMakeFiles/gkl_pairhmm_omp.dir/IntelPairHmm.cc.o CMakeFiles/gkl_pairhmm_omp.dir/avx_impl.cc.o CMakeFiles/gkl_pairhmm_omp.dir/avx512_impl.cc.o CMakeFiles/gkl_pairhmm_omp.dir/pairhmm_common.cc.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib: -fopenmp=libomp --- src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/all --- /usr/local/libexec/ccache/c++ -fPIC -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FORTIFY_SOURCE=2 -O3 -Wformat -Werror=format-security -Wconversion -Wfloat-conversion -Wbool-compare -fstack-protector-all -fno-strict-overflow -fno-delete-null-pointer-checks -fwrapv -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -Xlinker --dependency-file=CMakeFiles/gkl_smithwaterman.dir/link.d -static-libstdc++ -static-libgcc -Wl,-z,now -Wl,--no-as-needed -shared -Wl,-soname,libgkl_smithwaterman.so -o libgkl_smithwaterman.so CMakeFiles/gkl_smithwaterman.dir/IntelSmithWaterman.cc.o CMakeFiles/gkl_smithwaterman.dir/avx2_impl.cc.o CMakeFiles/gkl_smithwaterman.dir/avx512_impl.cc.o CMakeFiles/gkl_smithwaterman.dir/smithwaterman_common.cc.o -L/usr/local/lib -Wl,-rpath,:::::::::::::: [ 82%] Built target gkl_smithwaterman --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- [ 82%] Built target gkl_pairhmm_omp --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- Building static library libz.a version 1.2.13 with cc. Checking for size_t... Yes. Checking for off64_t... Yes. Checking for fseeko... Yes. Checking for strerror... Yes. Checking for unistd.h... Yes. Checking for stdarg.h... Yes. Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf(). Checking for vsnprintf() in stdio.h... Yes. Checking for return value of vsnprintf()... Yes. Checking for attribute(visibility) support... Yes. cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-build && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-configure --- src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-build --- [ 85%] Performing build step for 'otc_zlibExternal' cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-build && /usr/bin/make --- example64.o --- --- minigzip64.o --- --- example.o --- --- adler32.o --- --- crc32.o --- --- crc_folding.o --- --- deflate_quick.o --- --- deflate_medium.o --- --- deflate.o --- --- infback.o --- --- inffast.o --- --- inflate.o --- --- inftrees.o --- --- match.o --- --- slide_sse.o --- --- trees.o --- --- x86.o --- --- zutil.o --- --- compress.o --- --- uncompr.o --- --- gzclose.o --- --- gzlib.o --- --- gzread.o --- --- gzwrite.o --- --- minigzip.o --- --- compress.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o compress.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/compress.c /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/compress.c:22:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 22 | int ZEXPORT compress2(dest, destLen, source, sourceLen, level) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/compress.c:68:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 68 | int ZEXPORT compress(dest, destLen, source, sourceLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/compress.c:81:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 81 | uLong ZEXPORT compressBound(sourceLen) | ^ 3 warnings generated. --- zutil.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o zutil.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/zutil.c /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/zutil.c:135:22: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 135 | const char * ZEXPORT zError(err) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/zutil.c:307:22: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 307 | voidpf ZLIB_INTERNAL zcalloc(opaque, items, size) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/zutil.c:317:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 317 | void ZLIB_INTERNAL zcfree(opaque, ptr) | ^ 3 warnings generated. --- trees.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o trees.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:375:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 375 | void ZLIB_INTERNAL _tr_init(s) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:403:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 403 | local void init_block(s) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:447:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 447 | local void pqdownheap(s, tree, k) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:482:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 482 | local void gen_bitlen(s, desc) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:568:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 568 | local void gen_codes(tree, max_code, bl_count) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:611:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 611 | local void build_tree(s, desc) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:699:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 699 | local void scan_tree(s, tree, max_code) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:744:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 744 | local void send_tree(s, tree, max_code) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:795:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 795 | local int build_bl_tree(s) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:830:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 830 | local void send_all_trees(s, lcodes, dcodes, blcodes) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:859:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 859 | void ZLIB_INTERNAL _tr_stored_block(s, buf, stored_len, last) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:883:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 883 | void ZLIB_INTERNAL _tr_flush_bits(s) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:893:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 893 | void ZLIB_INTERNAL _tr_align(s) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:908:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 908 | void ZLIB_INTERNAL _tr_flush_block(s, buf, stored_len, last) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:1010:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1010 | int ZLIB_INTERNAL _tr_tally(s, dist, lc) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:1038:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1038 | local void compress_block(s, ltree, dtree) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:1098:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1098 | local int detect_data_type(s) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:1132:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1132 | local unsigned bi_reverse(code, len) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:1147:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1147 | local void bi_flush(s) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/trees.c:1164:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1164 | ZLIB_INTERNAL void bi_windup(s) | ^ 20 warnings generated. --- slide_sse.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -msse2 -c -o slide_sse.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/slide_sse.c --- match.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o match.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/match.c --- inftrees.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o inftrees.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inftrees.c /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inftrees.c:32:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 32 | int ZLIB_INTERNAL inflate_table(type, lens, codes, table, bits, work) | ^ 1 warning generated. --- inffast.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o inffast.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inffast.c /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inffast.c:50:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 50 | void ZLIB_INTERNAL inflate_fast(strm, start) | ^ 1 warning generated. --- crc32.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o crc32.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:126:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 126 | local z_word_t byte_swap(word) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:551:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 551 | local z_crc_t multmodp(a, b) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:575:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 575 | local z_crc_t x2nmodp(n, k) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:726:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 726 | local z_crc_t crc_word(data) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:735:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 735 | local z_word_t crc_word_big(data) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:748:23: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 748 | unsigned long ZEXPORT crc32_z(crc, buf, len) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1072:23: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1072 | unsigned long ZEXPORT crc32(crc, buf, len) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1081:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1081 | uLong ZEXPORT crc32_combine64(crc1, crc2, len2) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1093:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1093 | uLong ZEXPORT crc32_combine(crc1, crc2, len2) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1102:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1102 | uLong ZEXPORT crc32_combine_gen64(len2) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1112:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1112 | uLong ZEXPORT crc32_combine_gen(len2) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1119:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1119 | uLong ZEXPORT crc32_combine_op(crc1, crc2, op) | ^ 12 warnings generated. --- adler32.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o adler32.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/adler32.c /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/adler32.c:63:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 63 | uLong ZEXPORT adler32_z(adler, buf, len) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/adler32.c:150:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 150 | uLong ZEXPORT adler32(adler, buf, len) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/adler32.c:159:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 159 | local uLong adler32_combine_(adler1, adler2, len2) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/adler32.c:188:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 188 | uLong ZEXPORT adler32_combine(adler1, adler2, len2) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/adler32.c:196:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 196 | uLong ZEXPORT adler32_combine64(adler1, adler2, len2) | ^ 5 warnings generated. --- example.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -I/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/ -c -o example.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:88:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 88 | void test_compress(compr, comprLen, uncompr, uncomprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:114:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 114 | void test_gzio(fname, uncompr, uncomprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:200:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 200 | void test_deflate(compr, comprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:238:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 238 | void test_inflate(compr, comprLen, uncompr, uncomprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:279:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 279 | void test_large_deflate(compr, comprLen, uncompr, uncomprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:334:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 334 | void test_large_inflate(compr, comprLen, uncompr, uncomprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:375:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 375 | void test_flush(compr, comprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:413:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 413 | void test_sync(compr, comprLen, uncompr, uncomprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:456:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 456 | void test_dict_deflate(compr, comprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:493:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 493 | void test_dict_inflate(compr, comprLen, uncompr, uncomprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:544:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 544 | int main(argc, argv) | ^ 11 warnings generated. --- minigzip64.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -I/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/ -D_FILE_OFFSET_BITS=64 -c -o minigzip64.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:351:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 351 | void error(msg) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:362:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 362 | void gz_compress(in, out) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:430:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 430 | void gz_uncompress(in, out) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:457:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 457 | void file_compress(file, mode) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:496:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 496 | void file_uncompress(file) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:556:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 556 | int main(argc, argv) | ^ 6 warnings generated. --- example64.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -I/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/ -D_FILE_OFFSET_BITS=64 -c -o example64.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:88:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 88 | void test_compress(compr, comprLen, uncompr, uncomprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:114:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 114 | void test_gzio(fname, uncompr, uncomprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:200:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 200 | void test_deflate(compr, comprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:238:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 238 | void test_inflate(compr, comprLen, uncompr, uncomprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:279:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 279 | void test_large_deflate(compr, comprLen, uncompr, uncomprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:334:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 334 | void test_large_inflate(compr, comprLen, uncompr, uncomprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:375:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 375 | void test_flush(compr, comprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:413:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 413 | void test_sync(compr, comprLen, uncompr, uncomprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:456:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 456 | void test_dict_deflate(compr, comprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:493:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 493 | void test_dict_inflate(compr, comprLen, uncompr, uncomprLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:544:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 544 | int main(argc, argv) | ^ 11 warnings generated. --- gzclose.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o gzclose.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzclose.c --- gzlib.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o gzlib.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c --- gzread.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o gzread.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c --- x86.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o x86.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/x86.c --- crc_folding.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -mpclmul -msse4 -c -o crc_folding.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc_folding.c --- deflate_quick.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -msse4 -c -o deflate_quick.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate_quick.c --- deflate_medium.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o deflate_medium.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate_medium.c --- deflate.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o deflate.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c --- infback.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o infback.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/infback.c /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/infback.c:28:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 28 | int ZEXPORT inflateBackInit_(strm, windowBits, window, version, stream_size) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/infback.c:83:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 83 | local void fixedtables(state) | ^ --- inflate.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o inflate.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:105:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 105 | local int inflateStateCheck(strm) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:119:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 119 | int ZEXPORT inflateResetKeep(strm) | ^ --- uncompr.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o uncompr.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/uncompr.c --- infback.o --- /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/infback.c:251:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 251 | int ZEXPORT inflateBack(strm, in, in_desc, out, out_desc) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/infback.c:625:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 625 | int ZEXPORT inflateBackEnd(strm) | ^ 4 warnings generated. --- inflate.o --- /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:145:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 145 | int ZEXPORT inflateReset(strm) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:157:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 157 | int ZEXPORT inflateReset2(strm, windowBits) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:197:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 197 | int ZEXPORT inflateInit2_(strm, windowBits, version, stream_size) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:264:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 264 | int ZEXPORT inflateInit_(strm, version, stream_size) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:272:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 272 | int ZEXPORT inflatePrime(strm, bits, value) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:303:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 303 | local void fixedtables(state) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:421:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 421 | local int updatewindow(strm, end, copy) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:647:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 647 | int ZEXPORT inflate(strm, flush) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:1360:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1360 | int ZEXPORT inflateEnd(strm) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:1374:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1374 | int ZEXPORT inflateGetDictionary(strm, dictionary, dictLength) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:1397:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1397 | int ZEXPORT inflateSetDictionary(strm, dictionary, dictLength) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:1449:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1449 | int ZEXPORT inflateGetHeader(strm, head) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:1477:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1477 | local unsigned syncsearch(have, buf, len) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:1500:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1500 | int ZEXPORT inflateSync(strm) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:1558:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1558 | int ZEXPORT inflateSyncPoint(strm) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:1568:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1568 | int ZEXPORT inflateCopy(dest, source) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:1614:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1614 | int ZEXPORT inflateUndermine(strm, subvert) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:1632:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1632 | int ZEXPORT inflateValidate(strm, check) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:1647:14: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1647 | long ZEXPORT inflateMark(strm) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/inflate.c:1660:23: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1660 | unsigned long ZEXPORT inflateCodesUsed(strm) | ^ 22 warnings generated. --- minigzip.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -I/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/ -c -o minigzip.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c --- gzwrite.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o gzwrite.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzwrite.c --- deflate.o --- /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:196:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 196 | local void slide_hash_c(s) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:234:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 234 | int ZEXPORT deflateInit_(strm, level, version, stream_size) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:246:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 246 | int ZEXPORT deflateInit2_(strm, level, method, windowBits, memLevel, strategy, | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:412:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 412 | local int deflateStateCheck(strm) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:435:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 435 | int ZEXPORT deflateSetDictionary(strm, dictionary, dictLength) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:504:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 504 | int ZEXPORT deflateGetDictionary(strm, dictionary, dictLength) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:526:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 526 | int ZEXPORT deflateResetKeep(strm) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:570:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 570 | int ZEXPORT deflateReset(strm) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:582:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 582 | int ZEXPORT deflateSetHeader(strm, head) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:593:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 593 | int ZEXPORT deflatePending(strm, pending, bits) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:607:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 607 | int ZEXPORT deflatePrime(strm, bits, value) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:634:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 634 | int ZEXPORT deflateParams(strm, level, strategy) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:683:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 683 | int ZEXPORT deflateTune(strm, good_length, max_lazy, nice_length, max_chain) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:725:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 725 | uLong ZEXPORT deflateBound(strm, sourceLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:797:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 797 | local void putShortMSB(s, b) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:811:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 811 | ZLIB_INTERNAL void flush_pending(strm) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:844:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 844 | int ZEXPORT deflate(strm, flush) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:1170:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1170 | int ZEXPORT deflateEnd(strm) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:1196:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1196 | int ZEXPORT deflateCopy(dest, source) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:1255:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1255 | local unsigned read_buf(strm, buf, size) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:1294:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1294 | local void lm_init(s) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:1357:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1357 | ZLIB_INTERNAL void fill_window(s) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:1506:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1506 | local block_state deflate_stored(s, flush) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:1693:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1693 | local block_state deflate_fast(s, flush) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:1800:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1800 | local block_state deflate_slow(s, flush) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:1931:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1931 | local block_state deflate_rle(s, flush) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/deflate.c:2005:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2005 | local block_state deflate_huff(s, flush) | ^ 27 warnings generated. --- gzread.o --- /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c:21:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 21 | local int gz_load(state, buf, len, have) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c:56:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 56 | local int gz_avail(state) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c:91:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 91 | local int gz_look(state) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c:173:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 173 | local int gz_decomp(state) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c:227:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 227 | local int gz_fetch(state) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c:257:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 257 | local int gz_skip(state, len) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c:292:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 292 | local z_size_t gz_read(state, buf, len) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c:373:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 373 | int ZEXPORT gzread(file, buf, len) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c:409:18: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 409 | z_size_t ZEXPORT gzfread(buf, size, nitems, file) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c:445:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 445 | int ZEXPORT gzgetc(file) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c:472:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 472 | int ZEXPORT gzgetc_(file) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c:479:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 479 | int ZEXPORT gzungetc(c, file) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c:539:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 539 | char * ZEXPORT gzgets(file, buf, len) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c:603:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 603 | int ZEXPORT gzdirect(file) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzread.c:623:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 623 | int ZEXPORT gzclose_r(file) | ^ 15 warnings generated. --- gzwrite.o --- /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzwrite.c:17:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 17 | local int gz_init(state) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzwrite.c:73:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 73 | local int gz_comp(state, flush) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzwrite.c:154:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 154 | local int gz_zero(state, len) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzwrite.c:187:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 187 | local z_size_t gz_write(state, buf, len) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzwrite.c:255:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 255 | int ZEXPORT gzwrite(file, buf, len) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzwrite.c:283:18: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 283 | z_size_t ZEXPORT gzfwrite(buf, size, nitems, file) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzwrite.c:313:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 313 | int ZEXPORT gzputc(file, c) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzwrite.c:361:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 361 | int ZEXPORT gzputs(file, s) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzwrite.c:565:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 565 | int ZEXPORT gzflush(file, flush) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzwrite.c:597:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 597 | int ZEXPORT gzsetparams(file, level, strategy) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzwrite.c:639:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 639 | int ZEXPORT gzclose_w(file) | ^ 11 warnings generated. --- minigzip.o --- /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:351:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 351 | void error(msg) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:362:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 362 | void gz_compress(in, out) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:430:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 430 | void gz_uncompress(in, out) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:457:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 457 | void file_compress(file, mode) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:496:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 496 | void file_uncompress(file) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:556:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 556 | int main(argc, argv) | ^ 6 warnings generated. --- gzclose.o --- /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzclose.c:11:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 11 | int ZEXPORT gzclose(file) | ^ 1 warning generated. --- uncompr.o --- /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/uncompr.c:27:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 27 | int ZEXPORT uncompress2(dest, destLen, source, sourceLen) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/uncompr.c:86:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 86 | int ZEXPORT uncompress(dest, destLen, source, sourceLen) | ^ 2 warnings generated. --- gzlib.o --- /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:75:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 75 | local void gz_reset(state) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:93:14: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 93 | local gzFile gz_open(path, fd, mode) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:272:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 272 | gzFile ZEXPORT gzopen(path, mode) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:280:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 280 | gzFile ZEXPORT gzopen64(path, mode) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:288:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 288 | gzFile ZEXPORT gzdopen(fd, mode) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:318:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 318 | int ZEXPORT gzbuffer(file, size) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:345:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 345 | int ZEXPORT gzrewind(file) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:368:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 368 | z_off64_t ZEXPORT gzseek64(file, offset, whence) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:445:17: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 445 | z_off_t ZEXPORT gzseek(file, offset, whence) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:457:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 457 | z_off64_t ZEXPORT gztell64(file) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:474:17: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 474 | z_off_t ZEXPORT gztell(file) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:484:19: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 484 | z_off64_t ZEXPORT gzoffset64(file) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:507:17: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 507 | z_off_t ZEXPORT gzoffset(file) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:517:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 517 | int ZEXPORT gzeof(file) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:534:22: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 534 | const char * ZEXPORT gzerror(file, errnum) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:555:14: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 555 | void ZEXPORT gzclearerr(file) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/gzlib.c:581:20: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 581 | void ZLIB_INTERNAL gz_error(state, err, msg) | ^ 17 warnings generated. --- libz.a --- ar rc libz.a adler32.o crc32.o crc_folding.o deflate_quick.o deflate_medium.o deflate.o infback.o inffast.o inflate.o inftrees.o match.o slide_sse.o trees.o x86.o zutil.o compress.o uncompr.o gzclose.o gzlib.o gzread.o gzwrite.o --- example --- --- minigzip --- --- example64 --- --- minigzip64 --- --- example --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example example.o -L/usr/local/lib -L. libz.a --- minigzip --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip minigzip.o -L/usr/local/lib -L. libz.a --- example64 --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example64 example64.o -L/usr/local/lib -L. libz.a --- minigzip64 --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L/usr/local/lib -L. libz.a cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-build && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-build --- src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-install --- [ 88%] Performing install step for 'otc_zlibExternal' cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-build && /usr/bin/make install --- install-libs --- rm -f /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/lib/libz.a cp libz.a /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/lib chmod 644 /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/lib/libz.a rm -f /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/share/man/man3/zlib.3 cp /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/zlib.3 /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/share/man/man3 chmod 644 /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/share/man/man3/zlib.3 rm -f /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/lib/pkgconfig/zlib.pc cp zlib.pc /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/lib/pkgconfig chmod 644 /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/lib/pkgconfig/zlib.pc --- install --- rm -f /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/include/zlib.h /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/include/zconf.h cp /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/zlib.h zconf.h /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/include chmod 644 /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/include/zlib.h /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/include/zconf.h cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-build && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-install --- src/main/native/compression/CMakeFiles/otc_zlibExternal-complete --- [ 91%] Completed 'otc_zlibExternal' cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression && /usr/local/bin/cmake -E make_directory /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/CMakeFiles cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/CMakeFiles/otc_zlibExternal-complete cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-done [ 91%] Built target otc_zlibExternal --- src/main/native/compression/CMakeFiles/gkl_compression.dir/all --- /usr/bin/make -f src/main/native/compression/CMakeFiles/gkl_compression.dir/build.make src/main/native/compression/CMakeFiles/gkl_compression.dir/depend --- src/main/native/compression/CMakeFiles/gkl_compression.dir/depend --- cd /wrkdirs/usr/ports/biology/gkl/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1 /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression /wrkdirs/usr/ports/biology/gkl/work/.build /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/CMakeFiles/gkl_compression.dir/DependInfo.cmake /usr/bin/make -f src/main/native/compression/CMakeFiles/gkl_compression.dir/build.make src/main/native/compression/CMakeFiles/gkl_compression.dir/build --- src/main/native/compression/CMakeFiles/gkl_compression.dir/IntelDeflater.cc.o --- --- src/main/native/compression/CMakeFiles/gkl_compression.dir/IntelInflater.cc.o --- --- src/main/native/compression/CMakeFiles/gkl_compression.dir/IntelDeflater.cc.o --- [ 94%] Building CXX object src/main/native/compression/CMakeFiles/gkl_compression.dir/IntelDeflater.cc.o cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression && /usr/local/libexec/ccache/c++ -Dgkl_compression_EXPORTS -I/usr/local/openjdk8/include -I/usr/local/openjdk8/include/freebsd -I/wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/isa-l-master/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FORTIFY_SOURCE=2 -O3 -Wformat -Werror=format-security -Wconversion -Wfloat-conversion -Wbool-compare -fstack-protector-all -fno-strict-overflow -fno-delete-null-pointer-checks -fwrapv -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/main/native/compression/CMakeFiles/gkl_compression.dir/IntelDeflater.cc.o -MF CMakeFiles/gkl_compression.dir/IntelDeflater.cc.o.d -o CMakeFiles/gkl_compression.dir/IntelDeflater.cc.o -c /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/IntelDeflater.cc --- src/main/native/compression/CMakeFiles/gkl_compression.dir/IntelInflater.cc.o --- [ 97%] Building CXX object src/main/native/compression/CMakeFiles/gkl_compression.dir/IntelInflater.cc.o cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression && /usr/local/libexec/ccache/c++ -Dgkl_compression_EXPORTS -I/usr/local/openjdk8/include -I/usr/local/openjdk8/include/freebsd -I/wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/isa-l-master/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FORTIFY_SOURCE=2 -O3 -Wformat -Werror=format-security -Wconversion -Wfloat-conversion -Wbool-compare -fstack-protector-all -fno-strict-overflow -fno-delete-null-pointer-checks -fwrapv -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/main/native/compression/CMakeFiles/gkl_compression.dir/IntelInflater.cc.o -MF CMakeFiles/gkl_compression.dir/IntelInflater.cc.o.d -o CMakeFiles/gkl_compression.dir/IntelInflater.cc.o -c /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/IntelInflater.cc c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/IntelInflater.cc:214:44: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion] 214 | int bytes_out = outputBufferLength - lz_stream->avail_out; | ~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/IntelInflater.cc:214:25: warning: implicit conversion changes signedness: 'jint' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 214 | int bytes_out = outputBufferLength - lz_stream->avail_out; | ^~~~~~~~~~~~~~~~~~ ~ 3 warnings generated. --- src/main/native/compression/CMakeFiles/gkl_compression.dir/IntelDeflater.cc.o --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/IntelDeflater.cc:95:35: warning: implicit conversion changes signedness: 'jint' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 95 | lz_stream->level = level; | ~ ^~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/IntelDeflater.cc:206:31: warning: implicit conversion changes signedness: 'jint' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 206 | lz_stream->avail_in = inputBufferLength; | ~ ^~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/IntelDeflater.cc:209:32: warning: implicit conversion changes signedness: 'jint' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 209 | lz_stream->avail_out = outputBufferLength ; | ~ ^~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/IntelDeflater.cc:265:30: warning: implicit conversion changes signedness: 'jint' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion] 265 | uint32_t bytes_out = outputBufferLength - lz_stream->avail_out; | ^~~~~~~~~~~~~~~~~~ ~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/IntelDeflater.cc:274:16: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'jint' (aka 'int') [-Wsign-conversion] 274 | return bytes_out; | ~~~~~~ ^~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/IntelDeflater.cc:351:45: warning: implicit conversion changes signedness: 'uInt' (aka 'unsigned int') to 'int' [-Wsign-conversion] 351 | int bytes_out = outputBufferLength - lz_stream->avail_out; | ~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/IntelDeflater.cc:351:26: warning: implicit conversion changes signedness: 'jint' (aka 'int') to 'uInt' (aka 'unsigned int') [-Wsign-conversion] 351 | int bytes_out = outputBufferLength - lz_stream->avail_out; | ^~~~~~~~~~~~~~~~~~ ~ 8 warnings generated. --- src/main/native/compression/libgkl_compression.so --- [100%] Linking CXX shared library libgkl_compression.so cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gkl_compression.dir/link.txt --verbose=1 c++: warning: argument unused during compilation: '-static-libstdc++' [-Wunused-command-line-argument] c++: warning: argument unused during compilation: '-static-libgcc' [-Wunused-command-line-argument] /usr/local/libexec/ccache/c++ -fPIC -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FORTIFY_SOURCE=2 -O3 -Wformat -Werror=format-security -Wconversion -Wfloat-conversion -Wbool-compare -fstack-protector-all -fno-strict-overflow -fno-delete-null-pointer-checks -fwrapv -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -Xlinker --dependency-file=CMakeFiles/gkl_compression.dir/link.d -static-libstdc++ -static-libgcc -Wl,-z,now -shared -Wl,-soname,libgkl_compression.so -o libgkl_compression.so CMakeFiles/gkl_compression.dir/IntelDeflater.cc.o CMakeFiles/gkl_compression.dir/IntelInflater.cc.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib: otc_zlibExternal-prefix/lib/libz.a -lisal [100%] Built target gkl_compression /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/gkl/work/.build/CMakeFiles 0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gkl-0.9.1_1 depends on file: /usr/local/openjdk8/bin/java - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for gkl-0.9.1_1 ===> Generating temporary packing list /usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1 -B/wrkdirs/usr/ports/biology/gkl/work/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/gkl/work/.build/CMakeFiles /wrkdirs/usr/ports/biology/gkl/work/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/build.make src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/depend cd /wrkdirs/usr/ports/biology/gkl/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1 /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression /wrkdirs/usr/ports/biology/gkl/work/.build /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/DependInfo.cmake /usr/bin/make -f src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/build.make src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/build [ 23%] Built target otc_zlibExternal /usr/bin/make -f src/main/native/compression/CMakeFiles/gkl_compression.dir/build.make src/main/native/compression/CMakeFiles/gkl_compression.dir/depend cd /wrkdirs/usr/ports/biology/gkl/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1 /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression /wrkdirs/usr/ports/biology/gkl/work/.build /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/CMakeFiles/gkl_compression.dir/DependInfo.cmake /usr/bin/make -f src/main/native/compression/CMakeFiles/gkl_compression.dir/build.make src/main/native/compression/CMakeFiles/gkl_compression.dir/build [ 32%] Built target gkl_compression /usr/bin/make -f src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/build.make src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/depend cd /wrkdirs/usr/ports/biology/gkl/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1 /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm /wrkdirs/usr/ports/biology/gkl/work/.build /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/DependInfo.cmake /usr/bin/make -f src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/build.make src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/build [ 47%] Built target gkl_pairhmm /usr/bin/make -f src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/build.make src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/depend cd /wrkdirs/usr/ports/biology/gkl/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1 /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm /wrkdirs/usr/ports/biology/gkl/work/.build /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/DependInfo.cmake /usr/bin/make -f src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/build.make src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/build [ 61%] Built target gkl_pairhmm_omp /usr/bin/make -f src/main/native/utils/CMakeFiles/gkl_utils.dir/build.make src/main/native/utils/CMakeFiles/gkl_utils.dir/depend cd /wrkdirs/usr/ports/biology/gkl/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1 /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/utils /wrkdirs/usr/ports/biology/gkl/work/.build /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/utils /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/utils/CMakeFiles/gkl_utils.dir/DependInfo.cmake /usr/bin/make -f src/main/native/utils/CMakeFiles/gkl_utils.dir/build.make src/main/native/utils/CMakeFiles/gkl_utils.dir/build [ 67%] Built target gkl_utils /usr/bin/make -f src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/build.make src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/depend cd /wrkdirs/usr/ports/biology/gkl/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1 /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/smithwaterman /wrkdirs/usr/ports/biology/gkl/work/.build /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/smithwaterman /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/DependInfo.cmake /usr/bin/make -f src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/build.make src/main/native/smithwaterman/CMakeFiles/gkl_smithwaterman.dir/build [ 82%] Built target gkl_smithwaterman /usr/bin/make -f src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/build.make src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/depend cd /wrkdirs/usr/ports/biology/gkl/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1 /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pdhmm /wrkdirs/usr/ports/biology/gkl/work/.build /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pdhmm /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/DependInfo.cmake /usr/bin/make -f src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/build.make src/main/native/pdhmm/CMakeFiles/gkl_pdhmm.dir/build [100%] Built target gkl_pdhmm /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/gkl/work/.build/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall Installing the project stripped... /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/gkl/work/stage/usr/local/lib/libgkl_compression.so -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/biology/gkl/work/stage/usr/local/lib/libgkl_compression.so" to "/usr/local/lib" -- Installing: /wrkdirs/usr/ports/biology/gkl/work/stage/usr/local/lib/libgkl_pairhmm.so -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/biology/gkl/work/stage/usr/local/lib/libgkl_pairhmm.so" to "/usr/local/lib" -- Installing: /wrkdirs/usr/ports/biology/gkl/work/stage/usr/local/lib/libgkl_pairhmm_omp.so -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/biology/gkl/work/stage/usr/local/lib/libgkl_pairhmm_omp.so" to "/usr/local/lib" -- Installing: /wrkdirs/usr/ports/biology/gkl/work/stage/usr/local/lib/libgkl_utils.so -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/biology/gkl/work/stage/usr/local/lib/libgkl_utils.so" to "/usr/local/lib" -- Installing: /wrkdirs/usr/ports/biology/gkl/work/stage/usr/local/lib/libgkl_smithwaterman.so -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/biology/gkl/work/stage/usr/local/lib/libgkl_smithwaterman.so" to "/usr/local/lib" -- Installing: /wrkdirs/usr/ports/biology/gkl/work/stage/usr/local/lib/libgkl_pdhmm.so -- Set non-toolchain portion of runtime path of "/wrkdirs/usr/ports/biology/gkl/work/stage/usr/local/lib/libgkl_pdhmm.so" to "/usr/local/lib" ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-03-18T17:45:18+0000' 'PKG_NOTE_ports_top_git_hash=8c988f802ea2' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=693b58e8e410' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for gkl-0.9.1_1 ===> Building gkl-0.9.1_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for gkl-0.9.1_1 build of biology/gkl | gkl-0.9.1_1 ended at Wed Mar 18 13:45:38 EDT 2026 build time: 00:00:24