=>> Building biology/sra-tools build started at Thu Feb 19 10:59:57 EST 2026 port directory: /usr/ports/biology/sra-tools package name: sra-tools-3.3.0_2 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p3 FreeBSD 15.0-RELEASE-p3 1500068 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2357 Jan 15 19:47 /usr/ports/biology/sra-tools/Makefile Ports top last git commit: eac71dbf758c Ports top unclean checkout: no Port dir last git commit: aff412a94985 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 12 ---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/12/.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--- ===> The following configuration options are available for sra-tools-3.3.0_2: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/sra-tools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/sra-tools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/sra-tools/work/.cache HOME=/wrkdirs/usr/ports/biology/sra-tools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/sra-tools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/sra-tools/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/sra-tools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/sra-tools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/sra-tools/work/.cache HOME=/wrkdirs/usr/ports/biology/sra-tools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/sra-tools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/sra-tools/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 DESTDIR=/wrkdirs/usr/ports/biology/sra-tools/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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-- PORTVERSION=3.3.0 PORTEXAMPLES="" 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/sra-tools" EXAMPLESDIR="share/examples/sra-tools" DATADIR="share/sra-tools" WWWDIR="www/sra-tools" ETCDIR="etc/sra-tools" --End PLIST_SUB-- --SUB_LIST-- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="17" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/sra-tools DOCSDIR=/usr/local/share/doc/sra-tools EXAMPLESDIR=/usr/local/share/examples/sra-tools WWWDIR=/usr/local/www/sra-tools ETCDIR=/usr/local/etc/sra-tools --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 ===> sra-tools-3.3.0_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... done ===> sra-tools-3.3.0_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of sra-tools-3.3.0_2 =========================================================================== =================================================== ===== 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 sra-tools-3.3.0_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by sra-tools-3.3.0_2 for building => SHA256 Checksum OK for ncbi-sra-tools-3.3.0_GH0.tar.gz. => SHA256 Checksum OK for ncbi-ncbi-vdb-3.3.0_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 sra-tools-3.3.0_2 for building ===> Extracting for sra-tools-3.3.0_2 => SHA256 Checksum OK for ncbi-sra-tools-3.3.0_GH0.tar.gz. => SHA256 Checksum OK for ncbi-ncbi-vdb-3.3.0_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 sra-tools-3.3.0_2 ===> Applying FreeBSD patches for sra-tools-3.3.0_2 from /usr/ports/biology/sra-tools/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> sra-tools-3.3.0_2 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.3.9.pkg [pkg.DaveG.ca] Installing bash-5.3.9... [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 bash-5.3.9: .......... done ===> sra-tools-3.3.0_2 depends on executable: bash - found ===> Returning to build of sra-tools-3.3.0_2 ===> sra-tools-3.3.0_2 depends on executable: bison - not found ===> Installing existing package /packages/All/bison-3.8.2_2,1.pkg [pkg.DaveG.ca] Installing bison-3.8.2_2,1... [pkg.DaveG.ca] `-- Installing libtextstyle-0.26... [pkg.DaveG.ca] `-- Extracting libtextstyle-0.26: .......... done [pkg.DaveG.ca] `-- Installing m4-1.4.20,1... [pkg.DaveG.ca] `-- Extracting m4-1.4.20,1: .......... done [pkg.DaveG.ca] Extracting bison-3.8.2_2,1: .......... done ===> sra-tools-3.3.0_2 depends on executable: bison - found ===> Returning to build of sra-tools-3.3.0_2 ===> sra-tools-3.3.0_2 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-1.4.1... [pkg.DaveG.ca] | `-- Extracting libunistring-1.4.1: .......... 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 ===> sra-tools-3.3.0_2 depends on file: /usr/local/bin/cmake - found ===> Returning to build of sra-tools-3.3.0_2 ===> sra-tools-3.3.0_2 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.13.2,4.pkg [pkg.DaveG.ca] Installing ninja-1.13.2,4... [pkg.DaveG.ca] `-- Installing python311-3.11.14_2... [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | `-- Installing readline-8.3.3... [pkg.DaveG.ca] | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] `-- Extracting python311-3.11.14_2: .......... done [pkg.DaveG.ca] Extracting ninja-1.13.2,4: ..... done ===== Message from python311-3.11.14_2: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> sra-tools-3.3.0_2 depends on executable: ninja - found ===> Returning to build of sra-tools-3.3.0_2 ===> sra-tools-3.3.0_2 depends on file: /usr/local/openjdk17/bin/java - not found ===> Installing existing package /packages/All/openjdk17-17.0.18+8.1.pkg [pkg.DaveG.ca] Installing openjdk17-17.0.18+8.1... [pkg.DaveG.ca] `-- Installing alsa-lib-1.2.14... [pkg.DaveG.ca] `-- Extracting alsa-lib-1.2.14: .......... done [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-1.6.54... [pkg.DaveG.ca] | | `-- Extracting png-1.6.54: .......... done [pkg.DaveG.ca] | `-- Extracting freetype2-2.14.1: .......... done [pkg.DaveG.ca] `-- Extracting fontconfig-2.17.1,1: .......... done [pkg.DaveG.ca] `-- Installing giflib-5.2.2... [pkg.DaveG.ca] `-- Extracting giflib-5.2.2: .......... done [pkg.DaveG.ca] `-- Installing harfbuzz-12.3.2... [pkg.DaveG.ca] | `-- Installing glib-2.84.4,2... [pkg.DaveG.ca] | | `-- Installing libiconv-1.18_1... [pkg.DaveG.ca] | | `-- Extracting libiconv-1.18_1: .......... done [pkg.DaveG.ca] | | `-- Installing pcre2-10.47_1... [pkg.DaveG.ca] | | `-- Extracting pcre2-10.47_1: .......... done [pkg.DaveG.ca] | | `-- Installing py311-packaging-26.0... [pkg.DaveG.ca] | | `-- Extracting py311-packaging-26.0: .......... done [pkg.DaveG.ca] | `-- Extracting glib-2.84.4,2: .......... done [pkg.DaveG.ca] | `-- Installing graphite2-1.3.14... [pkg.DaveG.ca] | `-- Extracting graphite2-1.3.14: .......... done [pkg.DaveG.ca] `-- Extracting harfbuzz-12.3.2: .......... done [pkg.DaveG.ca] `-- Installing javavmwrapper-2.7.10... [pkg.DaveG.ca] `-- Extracting javavmwrapper-2.7.10: .......... done [pkg.DaveG.ca] `-- Installing jpeg-turbo-3.1.3... [pkg.DaveG.ca] `-- Extracting jpeg-turbo-3.1.3: .......... done [pkg.DaveG.ca] `-- Installing lcms2-2.18... [pkg.DaveG.ca] | `-- Installing tiff-4.7.1... [pkg.DaveG.ca] | | `-- Installing jbigkit-2.1_3... [pkg.DaveG.ca] | | `-- Extracting jbigkit-2.1_3: .......... done [pkg.DaveG.ca] | | `-- Installing lerc-4.0.0... [pkg.DaveG.ca] | | `-- Extracting lerc-4.0.0: ..... done [pkg.DaveG.ca] | | `-- Installing libdeflate-1.25... [pkg.DaveG.ca] | | `-- Extracting libdeflate-1.25: .......... done [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | `-- Extracting tiff-4.7.1: .......... done [pkg.DaveG.ca] `-- Extracting lcms2-2.18: .......... done [pkg.DaveG.ca] `-- Installing libX11-1.8.12,1... [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 libX11-1.8.12,1: .......... 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 libXrandr-1.5.4... [pkg.DaveG.ca] | `-- Installing libXrender-0.9.12... [pkg.DaveG.ca] | `-- Extracting libXrender-0.9.12: ....... done [pkg.DaveG.ca] `-- Extracting libXrandr-1.5.4: .......... 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 xorg-fonts-truetype-7.7_1... [pkg.DaveG.ca] | `-- Installing dejavu-2.37_4... [pkg.DaveG.ca] | | `-- Installing mkfontscale-1.2.3... [pkg.DaveG.ca] | | `-- Installing libfontenc-1.1.8... [pkg.DaveG.ca] | | `-- Extracting libfontenc-1.1.8: ...... done [pkg.DaveG.ca] | | `-- Extracting mkfontscale-1.2.3: .... done [pkg.DaveG.ca] | `-- Extracting dejavu-2.37_4: .......... done [pkg.DaveG.ca] | `-- Installing encodings-1.1.0,1... [pkg.DaveG.ca] | `-- Extracting encodings-1.1.0,1: .......... done [pkg.DaveG.ca] | `-- Installing font-bh-ttf-1.0.3_5... [pkg.DaveG.ca] | `-- Extracting font-bh-ttf-1.0.3_5: .......... done [pkg.DaveG.ca] | `-- Installing font-misc-ethiopic-1.0.4... [pkg.DaveG.ca] | `-- Extracting font-misc-ethiopic-1.0.4: ... done [pkg.DaveG.ca] | `-- Installing font-misc-meltho-1.0.3_5... [pkg.DaveG.ca] | `-- Extracting font-misc-meltho-1.0.3_5: .......... done [pkg.DaveG.ca] Extracting openjdk17-17.0.18+8.1: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== 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 openjdk17-17.0.18+8.1: -- 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 ===> sra-tools-3.3.0_2 depends on file: /usr/local/openjdk17/bin/java - found ===> Returning to build of sra-tools-3.3.0_2 ===> sra-tools-3.3.0_2 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. ===> sra-tools-3.3.0_2 depends on file: /usr/local/bin/ccache - found ===> Returning to build of sra-tools-3.3.0_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for sra-tools-3.3.0_2 cd /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build && cmake .. && make -- 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/bin/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/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at build/env.cmake:32 (cmake_policy): The OLD behavior for policy CMP0115 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. Call Stack (most recent call first): CMakeLists.txt:78 (include) VERSION=3.3.0 -- Found FLEX: /usr/bin/flex (found suitable version "2.6.4", minimum required is "2.6") -- Found BISON: /usr/local/bin/bison (found suitable version "3.8.2", minimum required is "3") -- Found Python3: /usr/local/bin/python3.11 (found version "3.11.14") found components: Interpreter -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) RUN_SANITIZER_TESTS: OFF Using local mbedtls headers from interfaces/ext/mbedtls Building local copy ext/mbedtls... -- Looking for gnu/libc-version.h -- Looking for gnu/libc-version.h - not found No mbedtls libs found installed in the system, using local copy... -- Configuring done (2.8s) -- Generating done (0.5s) -- Build files have been written to: /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build [ 0%] Building CXX object libs/ktst/CMakeFiles/ktst.dir/testenv.cpp.o [ 0%] Building CXX object libs/ktst/CMakeFiles/ktst.dir/testcase.cpp.o [ 0%] Building CXX object libs/ktst/CMakeFiles/ktst.dir/testrunner.cpp.o [ 1%] Building CXX object libs/ktst/CMakeFiles/ktst.dir/unix/systestenv.cpp.o [ 1%] Linking CXX static library ../../lib/libktst.a [ 1%] Built target ktst [ 2%] Building C object libs/align/CMakeFiles/ncbi-bam.dir/bam.c.o /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/libs/align/bam.c:3665:30: warning: variable 'B' set but not used [-Wunused-but-set-variable] 3665 | unsigned B = i + 2; | ^ 1 warning generated. 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-p /wrkdirs/usr/ports/biology/sra-tools/work/.build CMAKE_VERSION=3.31.10 -- 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 build/env.cmake:34 (cmake_policy): The OLD behavior for policy CMP0115 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. Call Stack (most recent call first): CMakeLists.txt:62 (include) BUILD_TOOLS_INTERNAL=OFF BUILD_TOOLS_LOADERS=OFF BUILD_TOOLS_TEST_TOOLS=OFF TOOLS_ONLY=ON DYNAMIC_LINK=OFF VERSION=3.3.0 -- Found FLEX: /usr/bin/flex (found suitable version "2.6.4", minimum required is "2.6") -- Found BISON: /usr/local/bin/bison (found suitable version "3.8.2", minimum required is "3") -- Could NOT find LibXml2 (missing: LIBXML2_LIBRARY LIBXML2_INCLUDE_DIR) -- Found Java: /usr/local/openjdk17/bin/java (found version "17.0.18") found components: Development -- Found Python3: /usr/local/bin/python3.11 (found version "3.11.14") found components: Interpreter Using ncbi-vdb interfaces: /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces Using ncbi-vdb binary libraries: /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib LSB_RELEASE_ID_SHORT: -- Found Python3: /wrkdirs/usr/ports/biology/sra-tools/work/.build/venv/bin/python3 (found version "3.11.14") found components: Interpreter Development Development.Module Development.Embed Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (24.0) WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 2] Name could not be resolved at this time')': /simple/pip/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 2] Name could not be resolved at this time')': /simple/pip/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 2] Name could not be resolved at this time')': /simple/pip/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 2] Name could not be resolved at this time')': /simple/pip/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 2] Name could not be resolved at this time')': /simple/pip/ WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 2] Name could not be resolved at this time')': /simple/setuptools/ Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (79.0.1) WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 2] Name could not be resolved at this time')': /simple/setuptools/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 2] Name could not be resolved at this time')': /simple/setuptools/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 2] Name could not be resolved at this time')': /simple/setuptools/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 2] Name could not be resolved at this time')': /simple/setuptools/ WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 2] Name could not be resolved at this time')': /simple/wheel/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 2] Name could not be resolved at this time')': /simple/wheel/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 2] Name could not be resolved at this time')': /simple/wheel/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 2] Name could not be resolved at this time')': /simple/wheel/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 2] Name could not be resolved at this time')': /simple/wheel/ ERROR: Could not find a version that satisfies the requirement wheel (from versions: none) ERROR: No matching distribution found for wheel -- Looking for C++ include mbedtls/md.h -- Looking for C++ include mbedtls/md.h - not found RUN_SANITIZER_TESTS: OFF -- Found JNI: /usr/local/openjdk17/include found components: AWT JVM -- Configuring done (60.3s) -- Generating done (1.3s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_MODULE_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/sra-tools/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for sra-tools-3.3.0_2 [ 0% 64/424] /usr/local/libexec/ccache/cc -DBSD -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 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/usr/local/libexec/ccache/cc -DBSD -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o -MF ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o.d -o 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-I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c11 -fPIC -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o -MF ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o.d -o ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ncbi/ngs/CSRA1_ReferenceWindow.c [ 1% 69/424] /usr/local/libexec/ccache/cc -DBSD -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang/x86_64 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[ 76% 389/424] /usr/local/libexec/ccache/cc -DBSD -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/ref_inventory.c.o -MF tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/ref_inventory.c.o.d -o tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/ref_inventory.c.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/fasterq-dump/ref_inventory.c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/fasterq-dump/ref_inventory.c:912:22: warning: variable 'base_cnt' set but not used [-Wunused-but-set-variable] 912 | uint64_t base_cnt = 0; | ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/fasterq-dump/ref_inventory.c:913:22: warning: variable 'chunks' set but not used [-Wunused-but-set-variable] 913 | uint32_t chunks = 0; | ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/fasterq-dump/ref_inventory.c:943:22: warning: variable 'base_cnt' set but not used [-Wunused-but-set-variable] 943 | uint64_t base_cnt = 0; | ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/fasterq-dump/ref_inventory.c:944:22: warning: variable 'chunks' set but not used [-Wunused-but-set-variable] 944 | uint32_t chunks = 0; | ^ 4 warnings generated. 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[ 86% 410/424] cd /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/examples && /usr/local/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/local/share/cmake/Modules/UseJava/ClearClassFiles.cmake --log-level STATUS && /usr/local/openjdk17/bin/javac -classpath :/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/examples:/wrkdirs/usr/ports/biology/sra-tools/work/.build/lib:/wrkdirs/usr/ports/biology/sra-tools/work/.build/lib/ngs-java.jar -d /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir @/wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/java_sources && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/java_compiled_ngs-examples [ 86% 411/424] : 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&& /usr/local/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/local/share/cmake/Modules/UseJava/ClassFilelist.cmake [ 87% 412/424] : && /usr/local/libexec/ccache/c++ -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Xlinker --dependency-file=tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/link.d tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/cache-mgr.c.o -o bin/cache-mgr -L/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib -Wl,-rpath,/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib lib/libkapp.a ilib/libtk-version.a /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm && cd 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tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o -MF tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o.d -o tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/vdb-validate/check-corrupt.cpp [ 88% 413/424] : && /usr/local/libexec/ccache/c++ -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Xlinker --dependency-file=tools/external/sra-stat/CMakeFiles/sra-stat.dir/link.d tools/external/sra-stat/CMakeFiles/sra-stat.dir/assembly-statistics.c.o tools/external/sra-stat/CMakeFiles/sra-stat.dir/sra.c.o tools/external/sra-stat/CMakeFiles/sra-stat.dir/sra-stat.c.o -o bin/sra-stat -L/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib 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tools/external/ref-variation/CMakeFiles/var-expand.dir/common.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/ref-variation/common.cpp [ 88% 413/424] : && /usr/local/libexec/ccache/c++ -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Xlinker --dependency-file=tools/external/test-sra/CMakeFiles/test-sra.dir/link.d tools/external/test-sra/CMakeFiles/test-sra.dir/test-sra.c.o tools/external/test-sra/CMakeFiles/test-sra.dir/unix/PrintOS.c.o -o bin/test-sra -L/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib -Wl,-rpath,/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib lib/libkapp.a ilib/libascp.a ilib/libdiagnose.a ilib/libtk-version.a /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm && cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/bin && rm -f test-sra.3.3.0 && mv test-sra test-sra.3.3.0 && ln -f -s test-sra.3.3.0 test-sra.3 && ln -f -s test-sra.3 test-sra [ 89% 413/424] /usr/local/libexec/ccache/c++ -DBSD -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/vdb-config -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/util.cpp.o -MF tools/external/vdb-config/CMakeFiles/vdb-config.dir/util.cpp.o.d -o tools/external/vdb-config/CMakeFiles/vdb-config.dir/util.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/vdb-config/util.cpp [ 89% 413/424] cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir && /usr/local/openjdk17/bin/jar -cf /wrkdirs/usr/ports/biology/sra-tools/work/.build/lib/ngs-examples.jar @java_class_filelist && /usr/local/bin/cmake -D_JAVA_TARGET_DIR=/wrkdirs/usr/ports/biology/sra-tools/work/.build/lib -D_JAVA_TARGET_OUTPUT_NAME=ngs-examples.jar -D_JAVA_TARGET_OUTPUT_LINK= -P /usr/local/share/cmake/Modules/UseJava/Symlinks.cmake [ 89% 413/424] cd /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java && /usr/local/openjdk17/bin/javadoc -d /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc -sourcepath "/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java" gov.nih.nlm.ncbi.ngs ngs Loading source files for package gov.nih.nlm.ncbi.ngs... Loading source files for package ngs... Constructing Javadoc information... Creating destination directory: "/wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/" Building index for all the packages and classes... Standard Doclet version 17.0.18+8-1 Building tree for all the packages and classes... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Alignment.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:140: warning: no comment static int all = primaryAlignment | secondaryAlignment; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:176: warning: no comment static int clipLeft = 0; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:177: warning: no comment static int clipRight = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:132: warning: no comment static int maxMapQuality = 8; // pass alignments with mappingQuality <= param ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:131: warning: no comment static int minMapQuality = 4; // pass alignments with mappingQuality >= param ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:133: warning: no comment static int noWraparound = 16; // do not include leading wrapped around alignments to circular references ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:130: warning: no comment static int passDuplicates = 2; // either a PCR or optical duplicate ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:129: warning: no comment static int passFailed = 1; // reads rejected due to platform/vendor quality criteria ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:138: warning: no comment static int primaryAlignment = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:139: warning: no comment static int secondaryAlignment = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:134: warning: no comment static int startWithinSlice = 32; // change slice intersection criteria so that start pos is within slice ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/AlignmentIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ErrorMsg.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/ErrorMsg.java:49: warning: no comment public ErrorMsg () ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/ErrorMsg.java:53: warning: no comment public ErrorMsg ( String message ) ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/ErrorMsg.java:58: warning: no comment public ErrorMsg ( ErrorMsg obj ) ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Fragment.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/FragmentIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:29: warning: no comment public class LibDependencies { ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:34: warning: no comment public final static String NCBI_VDB = "ncbi-ngs"; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:30: warning: no comment public final static String NGS_SDK = "ngs-sdk"; ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:40: warning: no comment public class NGS ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:133: warning: no comment public static void main(String[] args) { ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Package.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Pileup.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEvent.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:118: warning: no comment static int alignment_minus_strand = 0x20; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:116: warning: no comment static int alignment_start = 0x80; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:117: warning: no comment static int alignment_stop = 0x40; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:98: warning: no comment static int deletion = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:104: warning: no comment static int insertion = 0x08; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:112: warning: no comment static int insertion_before_deletion = insertion | deletion; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:107: warning: no comment static int insertion_before_match = insertion | match; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:108: warning: no comment static int insertion_before_mismatch = insertion | mismatch; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:180: warning: no comment static int intron_minus = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:179: warning: no comment static int intron_plus = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:181: warning: no comment static int intron_unknown = 3; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:97: warning: no comment static int mismatch = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:191: warning: no comment static int read_gap = 5; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:186: warning: no comment static int read_overlap = 4; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:113: warning: no comment static int replacement = insertion_before_deletion; ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEventIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Read.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Read.java:35: warning: no comment public interface Read ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Read.java:79: warning: no comment static int aligned = fullyAligned | partiallyAligned; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Read.java:81: warning: no comment static int all = aligned | unaligned; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Read.java:78: warning: no comment static int partiallyAligned = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Read.java:80: warning: no comment static int unaligned = 4; ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadCollection.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroup.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroupIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadIterator.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/ReadIterator.java:34: warning: no comment public interface ReadIterator ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Reference.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReferenceIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReferenceSequence.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Statistics.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Statistics.java:41: warning: no comment static int int64 = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Statistics.java:43: warning: no comment static int real = 4; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Statistics.java:40: warning: no comment static int string = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Statistics.java:42: warning: no comment static int uint64 = 3; ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-summary.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/package-summary.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/package-tree.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/constant-values.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/serialized-form.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/overview-tree.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/index.html... Building index for all classes... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/allclasses-index.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/allpackages-index.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/index-all.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/overview-summary.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/help-doc.html... 44 warnings [ 89% 415/424] /usr/local/libexec/ccache/c++ -DBSD -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D__mod__=\"tools/ref-variation\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -MD -MT tools/external/ref-variation/CMakeFiles/ref-variation.dir/helper.cpp.o -MF tools/external/ref-variation/CMakeFiles/ref-variation.dir/helper.cpp.o.d -o tools/external/ref-variation/CMakeFiles/ref-variation.dir/helper.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/ref-variation/helper.cpp [ 90% 415/424] /usr/local/libexec/ccache/c++ -DBSD -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D__mod__=\"tools/var-expand\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -MD -MT tools/external/ref-variation/CMakeFiles/var-expand.dir/helper.cpp.o -MF tools/external/ref-variation/CMakeFiles/var-expand.dir/helper.cpp.o.d -o tools/external/ref-variation/CMakeFiles/var-expand.dir/helper.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/ref-variation/helper.cpp [ 90% 415/424] /usr/local/libexec/ccache/c++ -DBSD -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D__mod__=\"tools/vdb-config\" -Dx86_64 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-I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -MD -MT tools/external/ref-variation/CMakeFiles/ref-variation.dir/ref-variation.cpp.o -MF tools/external/ref-variation/CMakeFiles/ref-variation.dir/ref-variation.cpp.o.d -o tools/external/ref-variation/CMakeFiles/ref-variation.dir/ref-variation.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/ref-variation/ref-variation.cpp [ 90% 416/424] /usr/local/libexec/ccache/c++ -DBSD -DBUILD_PATH=\"/wrkdirs/usr/ports/biology/sra-tools/work/.build/bin\" -DNDEBUG -DPREFIX_PATH=\"\" -DUNIX -D_ARCH_BITS=64 -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces 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-Wl,-rpath,/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib ilib/libtk-version.a /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm && cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/bin && rm -f check-corrupt.3.3.0 && mv check-corrupt check-corrupt.3.3.0 && ln -f -s check-corrupt.3.3.0 check-corrupt.3 && ln -f -s check-corrupt.3 check-corrupt [ 91% 417/424] /usr/local/libexec/ccache/c++ -DBSD -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D__mod__=\"tools/var-expand\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -MD -MT tools/external/ref-variation/CMakeFiles/var-expand.dir/var-expand.cpp.o -MF tools/external/ref-variation/CMakeFiles/var-expand.dir/var-expand.cpp.o.d -o tools/external/ref-variation/CMakeFiles/var-expand.dir/var-expand.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/ref-variation/var-expand.cpp [ 91% 418/424] /usr/local/libexec/ccache/c++ -DBSD -DBUILD_PATH=\"/wrkdirs/usr/ports/biology/sra-tools/work/.build/bin\" -DNDEBUG -DPREFIX_PATH=\"\" -DUNIX -D_ARCH_BITS=64 -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o -MF tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o.d -o tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/driver-tool/file-path.posix.cpp [ 91% 418/424] /usr/local/libexec/ccache/c++ -DBSD -DBUILD_PATH=\"/wrkdirs/usr/ports/biology/sra-tools/work/.build/bin\" -DNDEBUG -DPREFIX_PATH=\"\" -DUNIX -D_ARCH_BITS=64 -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o -MF tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o.d -o tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/driver-tool/build-version.cpp [ 92% 418/424] cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc && sh -c /usr/local/openjdk17/bin/jar\ -cf\ /wrkdirs/usr/ports/biology/sra-tools/work/.build/lib/ngs-doc.jar\ . [ 92% 418/424] /usr/local/libexec/ccache/c++ -DBSD -DBUILD_PATH=\"/wrkdirs/usr/ports/biology/sra-tools/work/.build/bin\" -DNDEBUG -DPREFIX_PATH=\"\" -DUNIX -D_ARCH_BITS=64 -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/service.cpp.o -MF tools/external/driver-tool/CMakeFiles/sratools.dir/service.cpp.o.d -o tools/external/driver-tool/CMakeFiles/sratools.dir/service.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/driver-tool/service.cpp [ 92% 418/424] : && /usr/local/libexec/ccache/c++ -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Xlinker --dependency-file=tools/external/ref-variation/CMakeFiles/ref-variation.dir/link.d tools/external/ref-variation/CMakeFiles/ref-variation.dir/common.cpp.o tools/external/ref-variation/CMakeFiles/ref-variation.dir/helper.cpp.o tools/external/ref-variation/CMakeFiles/ref-variation.dir/ref-variation.cpp.o -o bin/ref-variation -L/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib -Wl,-rpath,/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib ilib/libtk-version.a lib/libkapp.a ilib/libngs-vdb.a lib/libncbi-ngs.a ilib/libloader.a /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm ilib/libtk-version.a ilib/libksrch.a && cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/bin && rm -f ref-variation.3.3.0 && mv ref-variation ref-variation.3.3.0 && ln -f -s ref-variation.3.3.0 ref-variation.3 && ln -f -s ref-variation.3 ref-variation [ 92% 418/424] cd /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java && sh -c /usr/local/openjdk17/bin/jar\ -cf\ /wrkdirs/usr/ports/biology/sra-tools/work/.build/lib/ngs-src.jar\ \ ngs/ErrorMsg.java\ ngs/Statistics.java\ ngs/Fragment.java\ ngs/FragmentIterator.java\ ngs/Read.java\ ngs/ReadIterator.java\ ngs/ReadGroup.java\ ngs/ReadGroupIterator.java\ ngs/Alignment.java\ ngs/AlignmentIterator.java\ ngs/PileupEvent.java\ ngs/PileupEventIterator.java\ ngs/Pileup.java\ ngs/PileupIterator.java\ ngs/Reference.java\ ngs/ReferenceIterator.java\ ngs/ReadCollection.java\ ngs/Package.java\ ngs/itf/Refcount.java\ ngs/itf/StatisticsItf.java\ ngs/itf/FragmentItf.java\ ngs/itf/FragmentIteratorItf.java\ ngs/itf/ReadItf.java\ ngs/itf/ReadIteratorItf.java\ ngs/itf/ReadGroupItf.java\ ngs/itf/ReadGroupIteratorItf.java\ ngs/itf/AlignmentItf.java\ ngs/itf/AlignmentIteratorItf.java\ ngs/itf/PileupEventItf.java\ ngs/itf/PileupEventIteratorItf.java\ ngs/itf/PileupItf.java\ ngs/itf/PileupIteratorItf.java\ ngs/itf/ReferenceItf.java\ ngs/itf/ReferenceIteratorItf.java\ ngs/itf/ReadCollectionItf.java\ gov/nih/nlm/ncbi/ngs/DownloadManager.java\ gov/nih/nlm/ncbi/ngs/FileCreator.java\ gov/nih/nlm/ncbi/ngs/HttpManager.java\ gov/nih/nlm/ncbi/ngs/LibDependencies.java\ gov/nih/nlm/ncbi/ngs/LibManager.java\ gov/nih/nlm/ncbi/ngs/LibPathIterator.java\ gov/nih/nlm/ncbi/ngs/LibVersionChecker.java\ gov/nih/nlm/ncbi/ngs/LMProperties.java\ gov/nih/nlm/ncbi/ngs/Logger.java\ gov/nih/nlm/ncbi/ngs/Manager.java\ gov/nih/nlm/ncbi/ngs/NGS.java\ gov/nih/nlm/ncbi/ngs/Version.java\ gov/nih/nlm/ncbi/ngs/error/LibraryLoadError.java\ gov/nih/nlm/ncbi/ngs/error/LibraryNotFoundError.java\ gov/nih/nlm/ncbi/ngs/error/LibraryIncompatibleVersionError.java\ gov/nih/nlm/ncbi/ngs/error/cause/ConnectionProblemCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/DownloadDisabledCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/InvalidLibraryCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/JvmErrorCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/LibraryLoadCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/OutdatedJarCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/PrereleaseReqLibCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/UnsupportedArchCause.java [ 93% 418/424] /usr/local/libexec/ccache/c++ -DBSD -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D__mod__=\"tools/ngs-pileup\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ncbi/ngs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -MD -MT tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o -MF tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o.d -o tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/ngs-pileup/ngs-pileup.cpp [ 93% 418/424] /usr/local/libexec/ccache/c++ -DBSD -DBUILD_PATH=\"/wrkdirs/usr/ports/biology/sra-tools/work/.build/bin\" -DNDEBUG -DPREFIX_PATH=\"\" -DUNIX -D_ARCH_BITS=64 -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -Wall -O2 -pipe 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-I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -fPIE -MD -MT libs/general-writer/CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o -MF libs/general-writer/CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o.d -o libs/general-writer/CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/general-writer/gw-dumper.cpp [ 94% 419/424] /usr/local/libexec/ccache/c++ -DBSD -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D__mod__=\"tools/ngs-pileup\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ncbi/ngs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -MD -MT tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/main.cpp.o -MF tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/main.cpp.o.d -o tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/main.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/ngs-pileup/main.cpp [ 94% 420/424] : && /usr/local/libexec/ccache/c++ -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Xlinker --dependency-file=tools/external/ref-variation/CMakeFiles/var-expand.dir/link.d tools/external/ref-variation/CMakeFiles/var-expand.dir/common.cpp.o tools/external/ref-variation/CMakeFiles/var-expand.dir/helper.cpp.o tools/external/ref-variation/CMakeFiles/var-expand.dir/var-expand.cpp.o -o bin/var-expand -L/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib -Wl,-rpath,/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib ilib/libtk-version.a lib/libkapp.a ilib/libngs-vdb.a lib/libncbi-ngs.a ilib/libloader.a /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread 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-I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o -MF tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o.d -o 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-I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o -MF tools/external/sra-search/CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o.d -o tools/external/sra-search/CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/sra-search/fragmentmatchiterator.cpp [ 97% 421/424] /usr/local/libexec/ccache/c++ -DBSD 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-I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o -MF tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o.d -o tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o -c /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/driver-tool/tool-args.cpp [ 97% 421/424] /usr/local/libexec/ccache/c++ -DBSD -DBUILD_PATH=\"/wrkdirs/usr/ports/biology/sra-tools/work/.build/bin\" -DNDEBUG -DPREFIX_PATH=\"\" -DUNIX -D_ARCH_BITS=64 -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces 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/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/tools/external/driver-tool/run-source.cpp [ 98% 421/424] : && /usr/local/libexec/ccache/c++ -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Xlinker --dependency-file=tools/external/sra-search/CMakeFiles/sra-search.dir/link.d tools/external/sra-search/CMakeFiles/sra-search.dir/main.cpp.o tools/external/sra-search/CMakeFiles/sra-search.dir/searchblock.cpp.o tools/external/sra-search/CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o tools/external/sra-search/CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o tools/external/sra-search/CMakeFiles/sra-search.dir/referencematchiterator.cpp.o tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o -o bin/sra-search -L/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib 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tools/external/driver-tool/CMakeFiles/sratools.dir/run-source.cpp.o tools/external/driver-tool/CMakeFiles/sratools.dir/proc.cpp.o tools/external/driver-tool/CMakeFiles/sratools.dir/uuid.cpp.o tools/external/driver-tool/CMakeFiles/sratools.dir/accession.cpp.o tools/external/driver-tool/CMakeFiles/sratools.dir/service.cpp.o tools/external/driver-tool/CMakeFiles/sratools.dir/json-parse.cpp.o tools/external/driver-tool/CMakeFiles/sratools.dir/SDL-response.cpp.o tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o tools/external/driver-tool/CMakeFiles/sratools.dir/proc.posix.cpp.o -o bin/sratools -L/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib -Wl,-rpath,/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm && cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/bin && rm -f sratools.3.3.0 && mv sratools sratools.3.3.0 && ln -f -s sratools.3.3.0 sratools.3 && ln -f -s sratools.3 sratools [ 99% 422/424] /usr/local/libexec/ccache/c++ -DBSD -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D__mod__=\"tools/sra-info\" -Dx86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/cc/clang/x86_64 -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/bsd -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/interfaces/os/unix -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-sdk -I/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/libs/inc -Wall 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=========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> sra-tools-3.3.0_2 depends on package: hdf5>0 - not found ===> Installing existing package /packages/All/hdf5-1.12.2_2,1.pkg [pkg.DaveG.ca] Installing hdf5-1.12.2_2,1... [pkg.DaveG.ca] `-- Installing gcc14-14.2.0_4... [pkg.DaveG.ca] | `-- Installing binutils-2.44,1... [pkg.DaveG.ca] | `-- Extracting binutils-2.44,1: .......... done [pkg.DaveG.ca] | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | `-- Installing mpc-1.3.1_1... [pkg.DaveG.ca] | | `-- Installing mpfr-4.2.2,1... [pkg.DaveG.ca] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg.DaveG.ca] | `-- Extracting mpc-1.3.1_1: ...... done [pkg.DaveG.ca] `-- Extracting gcc14-14.2.0_4: .......... done create symlink for gcc14 create symlink for gcc14 (world) create symlink for g++14 create symlink for g++14 (world) create symlink for cpp14 create symlink for cpp14 (world) [pkg.DaveG.ca] `-- Installing libaec-1.1.4... 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ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ngs/ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o -L/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib -Wl,-rpath,/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib ilib/libtk-version.a /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm && cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/lib && rm -f libncbi-ngs.so.3.3.0 && mv libncbi-ngs.so libncbi-ngs.so.3.3.0 && ln -f -s libncbi-ngs.so.3.3.0 libncbi-ngs.so.3 && ln -f -s libncbi-ngs.so.3 libncbi-ngs.so [ 45% 8/11] : && /usr/local/libexec/ccache/c++ -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Xlinker --dependency-file=tools/external/ref-variation/CMakeFiles/ref-variation.dir/link.d tools/external/ref-variation/CMakeFiles/ref-variation.dir/common.cpp.o tools/external/ref-variation/CMakeFiles/ref-variation.dir/helper.cpp.o tools/external/ref-variation/CMakeFiles/ref-variation.dir/ref-variation.cpp.o -o bin/ref-variation -L/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib -Wl,-rpath,/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib ilib/libtk-version.a lib/libkapp.a ilib/libngs-vdb.a lib/libncbi-ngs.a ilib/libloader.a /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm ilib/libtk-version.a ilib/libksrch.a && cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/bin && rm -f ref-variation.3.3.0 && mv ref-variation ref-variation.3.3.0 && ln -f -s ref-variation.3.3.0 ref-variation.3 && ln -f -s ref-variation.3 ref-variation [ 54% 8/11] : && /usr/local/libexec/ccache/c++ -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Xlinker --dependency-file=tools/external/ref-variation/CMakeFiles/var-expand.dir/link.d tools/external/ref-variation/CMakeFiles/var-expand.dir/common.cpp.o tools/external/ref-variation/CMakeFiles/var-expand.dir/helper.cpp.o tools/external/ref-variation/CMakeFiles/var-expand.dir/var-expand.cpp.o -o bin/var-expand -L/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib -Wl,-rpath,/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib ilib/libtk-version.a lib/libkapp.a ilib/libngs-vdb.a lib/libncbi-ngs.a ilib/libloader.a /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm ilib/libtk-version.a ilib/libksrch.a && cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/bin && rm -f var-expand.3.3.0 && mv var-expand var-expand.3.3.0 && ln -f -s var-expand.3.3.0 var-expand.3 && ln -f -s var-expand.3 var-expand [ 63% 8/11] : && /usr/local/libexec/ccache/c++ -Wall -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-unused-function -Wno-tautological-undefined-compare -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -Xlinker --dependency-file=tools/external/sra-search/CMakeFiles/sra-search.dir/link.d tools/external/sra-search/CMakeFiles/sra-search.dir/main.cpp.o tools/external/sra-search/CMakeFiles/sra-search.dir/searchblock.cpp.o tools/external/sra-search/CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o tools/external/sra-search/CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o tools/external/sra-search/CMakeFiles/sra-search.dir/referencematchiterator.cpp.o tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o -o bin/sra-search -L/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib -Wl,-rpath,/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib ilib/libngs-vdb.a lib/libncbi-ngs.a ilib/libtk-version.a lib/libkapp.a /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ncbi-vdb/build/lib/libncbi-vdb.a -lpthread -ldl -lm ilib/libtk-version.a ilib/libksrch.a && cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/bin && rm -f sra-search.3.3.0 && mv sra-search sra-search.3.3.0 && ln -f -s sra-search.3.3.0 sra-search.3 && ln -f -s sra-search.3 sra-search [ 72% 8/11] cd /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java && /usr/local/openjdk17/bin/javadoc -d /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc -sourcepath "/wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java" gov.nih.nlm.ncbi.ngs ngs Loading source files for package gov.nih.nlm.ncbi.ngs... Loading source files for package ngs... Constructing Javadoc information... Building index for all the packages and classes... Standard Doclet version 17.0.18+8-1 Building tree for all the packages and classes... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Alignment.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:140: warning: no comment static int all = primaryAlignment | secondaryAlignment; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:176: warning: no comment static int clipLeft = 0; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:177: warning: no comment static int clipRight = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:132: warning: no comment static int maxMapQuality = 8; // pass alignments with mappingQuality <= param ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:131: warning: no comment static int minMapQuality = 4; // pass alignments with mappingQuality >= param ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:133: warning: no comment static int noWraparound = 16; // do not include leading wrapped around alignments to circular references ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:130: warning: no comment static int passDuplicates = 2; // either a PCR or optical duplicate ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:129: warning: no comment static int passFailed = 1; // reads rejected due to platform/vendor quality criteria ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:138: warning: no comment static int primaryAlignment = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:139: warning: no comment static int secondaryAlignment = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Alignment.java:134: warning: no comment static int startWithinSlice = 32; // change slice intersection criteria so that start pos is within slice ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/AlignmentIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ErrorMsg.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/ErrorMsg.java:49: warning: no comment public ErrorMsg () ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/ErrorMsg.java:53: warning: no comment public ErrorMsg ( String message ) ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/ErrorMsg.java:58: warning: no comment public ErrorMsg ( ErrorMsg obj ) ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Fragment.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/FragmentIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:29: warning: no comment public class LibDependencies { ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:34: warning: no comment public final static String NCBI_VDB = "ncbi-ngs"; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:30: warning: no comment public final static String NGS_SDK = "ngs-sdk"; ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:40: warning: no comment public class NGS ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:133: warning: no comment public static void main(String[] args) { ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Package.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Pileup.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEvent.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:118: warning: no comment static int alignment_minus_strand = 0x20; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:116: warning: no comment static int alignment_start = 0x80; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:117: warning: no comment static int alignment_stop = 0x40; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:98: warning: no comment static int deletion = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:104: warning: no comment static int insertion = 0x08; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:112: warning: no comment static int insertion_before_deletion = insertion | deletion; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:107: warning: no comment static int insertion_before_match = insertion | match; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:108: warning: no comment static int insertion_before_mismatch = insertion | mismatch; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:180: warning: no comment static int intron_minus = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:179: warning: no comment static int intron_plus = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:181: warning: no comment static int intron_unknown = 3; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:97: warning: no comment static int mismatch = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:191: warning: no comment static int read_gap = 5; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:186: warning: no comment static int read_overlap = 4; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/PileupEvent.java:113: warning: no comment static int replacement = insertion_before_deletion; ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEventIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Read.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Read.java:35: warning: no comment public interface Read ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Read.java:79: warning: no comment static int aligned = fullyAligned | partiallyAligned; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Read.java:81: warning: no comment static int all = aligned | unaligned; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Read.java:78: warning: no comment static int partiallyAligned = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Read.java:80: warning: no comment static int unaligned = 4; ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadCollection.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroup.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroupIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadIterator.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/ReadIterator.java:34: warning: no comment public interface ReadIterator ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Reference.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReferenceIterator.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/ReferenceSequence.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/Statistics.html... /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Statistics.java:41: warning: no comment static int int64 = 2; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Statistics.java:43: warning: no comment static int real = 4; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Statistics.java:40: warning: no comment static int string = 1; ^ /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java/ngs/Statistics.java:42: warning: no comment static int uint64 = 3; ^ Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-summary.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/package-summary.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/ngs/package-tree.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/constant-values.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/serialized-form.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/overview-tree.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/index.html... Building index for all classes... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/allclasses-index.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/allpackages-index.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/index-all.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/overview-summary.html... Generating /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc/help-doc.html... 44 warnings [ 81% 10/11] cd /wrkdirs/usr/ports/biology/sra-tools/work/sra-tools-3.3.0/ngs/ngs-java && sh -c /usr/local/openjdk17/bin/jar\ -cf\ /wrkdirs/usr/ports/biology/sra-tools/work/.build/lib/ngs-src.jar\ \ ngs/ErrorMsg.java\ ngs/Statistics.java\ ngs/Fragment.java\ ngs/FragmentIterator.java\ ngs/Read.java\ ngs/ReadIterator.java\ ngs/ReadGroup.java\ ngs/ReadGroupIterator.java\ ngs/Alignment.java\ ngs/AlignmentIterator.java\ ngs/PileupEvent.java\ ngs/PileupEventIterator.java\ ngs/Pileup.java\ ngs/PileupIterator.java\ ngs/Reference.java\ ngs/ReferenceIterator.java\ ngs/ReadCollection.java\ ngs/Package.java\ ngs/itf/Refcount.java\ ngs/itf/StatisticsItf.java\ ngs/itf/FragmentItf.java\ ngs/itf/FragmentIteratorItf.java\ ngs/itf/ReadItf.java\ ngs/itf/ReadIteratorItf.java\ ngs/itf/ReadGroupItf.java\ ngs/itf/ReadGroupIteratorItf.java\ ngs/itf/AlignmentItf.java\ ngs/itf/AlignmentIteratorItf.java\ ngs/itf/PileupEventItf.java\ ngs/itf/PileupEventIteratorItf.java\ ngs/itf/PileupItf.java\ ngs/itf/PileupIteratorItf.java\ ngs/itf/ReferenceItf.java\ ngs/itf/ReferenceIteratorItf.java\ ngs/itf/ReadCollectionItf.java\ gov/nih/nlm/ncbi/ngs/DownloadManager.java\ gov/nih/nlm/ncbi/ngs/FileCreator.java\ gov/nih/nlm/ncbi/ngs/HttpManager.java\ gov/nih/nlm/ncbi/ngs/LibDependencies.java\ gov/nih/nlm/ncbi/ngs/LibManager.java\ gov/nih/nlm/ncbi/ngs/LibPathIterator.java\ gov/nih/nlm/ncbi/ngs/LibVersionChecker.java\ gov/nih/nlm/ncbi/ngs/LMProperties.java\ gov/nih/nlm/ncbi/ngs/Logger.java\ gov/nih/nlm/ncbi/ngs/Manager.java\ gov/nih/nlm/ncbi/ngs/NGS.java\ gov/nih/nlm/ncbi/ngs/Version.java\ gov/nih/nlm/ncbi/ngs/error/LibraryLoadError.java\ gov/nih/nlm/ncbi/ngs/error/LibraryNotFoundError.java\ gov/nih/nlm/ncbi/ngs/error/LibraryIncompatibleVersionError.java\ gov/nih/nlm/ncbi/ngs/error/cause/ConnectionProblemCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/DownloadDisabledCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/InvalidLibraryCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/JvmErrorCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/LibraryLoadCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/OutdatedJarCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/PrereleaseReqLibCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/UnsupportedArchCause.java [ 90% 10/11] cd /wrkdirs/usr/ports/biology/sra-tools/work/.build/ngs/ngs-java/javadoc/ngs-doc && sh -c /usr/local/openjdk17/bin/jar\ -cf\ /wrkdirs/usr/ports/biology/sra-tools/work/.build/lib/ngs-doc.jar\ . [ 90% 11/11] cd /wrkdirs/usr/ports/biology/sra-tools/work/.build && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" Updating /etc/profile.d/sra-tools.sh Updating /etc/profile.d/sra-tools.csh -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs-c++.a.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs-c++.a.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs-c++.a -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs-c++-static.a -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ncbi-vdb/NGS.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools/FragTest.cpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools/AlignTest.cpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools/AlignSliceTest.cpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools/PileupTest.cpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools/RefTest.cpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools/DumpReferenceFASTA.cpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools/expected.txt -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools/Makefile -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/examples/sra-tools/README.txt -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libngs-c++.a.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libngs-c++.a.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libngs-c++.a -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libngs-c++-static.a -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libngs-c++.so.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libngs-c++.so.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libngs-c++.so -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs.a.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs.a.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs.a -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs-static.a -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs.so.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs.so.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/libncbi-ngs.so -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/Statistics.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/PileupEvent.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/ReferenceIterator.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/ReadGroup.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/Pileup.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/Alignment.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/win -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/win/stdbool.h -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/win/atomic32.h -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/PileupEventIterator.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/Fragment.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/ReadGroupIterator.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/FragmentItf.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/ReadCollectionItf.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/ReferenceSequenceItf.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/Refcount.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/AlignmentItf.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/StringItf.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/defs.h -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/PileupItf.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/ReadItf.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/PileupEventItf.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/ReferenceItf.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/StatisticsItf.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/ErrorMsg.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/adapter/ReadGroupItf.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/ReferenceSequence.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/Read.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/AlignmentIterator.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/unix -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/unix/arm64 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/unix/arm64/atomic32.h -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/unix/fat86 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/unix/fat86/atomic32.h -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/unix/x86_64 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/unix/x86_64/atomic32.h -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/unix/i386 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/unix/i386/atomic32.h -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/StringRef.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/FragmentIterator.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/ReadIterator.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/inl -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/inl/Statistics.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/inl/PileupEvent.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/inl/ReferenceIterator.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/inl/ReadGroup.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/inl/Pileup.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/inl/Alignment.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/inl/PileupEventIterator.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/inl/Fragment.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/inl/ReadGroupIterator.hpp -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/include/ngs/inl/ReferenceSequence.hpp -- Installing: 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/wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-decrypt.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-decrypt.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-decrypt -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-encrypt.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-encrypt.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/vdb-encrypt -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/srapath -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/srapath.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/srapath-orig.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/srapath.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-stat.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-stat.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-stat -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/ngs-pileup.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/ngs-pileup.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/ngs-pileup -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/rcexplain.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/rcexplain.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/rcexplain -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/kdbmeta.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/kdbmeta.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/kdbmeta -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/align-info.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/align-info.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/align-info -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/ref-variation.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/ref-variation.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/ref-variation -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/var-expand.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/var-expand.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/var-expand -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-search.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-search.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-search -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/test-sra.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/test-sra.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/test-sra -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/cache-mgr.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/cache-mgr.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/cache-mgr -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sratools.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sratools.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sratools -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-info.3.3.0 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-info.3 -- Installing: /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/sra-info /usr/bin/strip /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/bin/*.3.3.0 /usr/bin/strip /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/lib64/*.3.3.0 /bin/mv /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/script-dir/jquery-[0-9]*.min.js /wrkdirs/usr/ports/biology/sra-tools/work/stage/usr/local/share/javadoc/ngs-doc/script-dir/jquery.min.js ====> Compressing man pages (compress-man) ===> Installing ldconfig configuration file =========================================================================== =================================================== ===== 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=2026-02-19T15:59:57+0000' 'PKG_NOTE_ports_top_git_hash=eac71dbf758c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=aff412a94985' '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 sra-tools-3.3.0_2 ===> Building sra-tools-3.3.0_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for sra-tools-3.3.0_2 build of biology/sra-tools | sra-tools-3.3.0_2 ended at Thu Feb 19 11:17:48 EST 2026 build time: 00:17:52