=>> Building biology/wise build started at Sun Jan 25 07:14:29 EST 2026 port directory: /usr/ports/biology/wise package name: wise-2.4.1_1 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: ports@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2350 Oct 16 2024 /usr/ports/biology/wise/Makefile Ports top last git commit: 076a295eb33c Ports top unclean checkout: no Port dir last git commit: 4485bd8221c2 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1305000 Job Id: 08 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p7 1305000 UNAME_r=13.5-RELEASE-p7 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_13_5_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_13_5_x64-HEAD-ALL/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_13_5_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_13_5_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 wise-2.4.1_1: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/wise/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/wise/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/wise/work/.cache HOME=/wrkdirs/usr/ports/biology/wise/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/wise/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/wise/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-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/wise/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/wise/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/wise/work/.cache HOME=/wrkdirs/usr/ports/biology/wise/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/wise/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/wise/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -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-- PORTDOCS="" PORTEXAMPLES="" GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" OSREL=13.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/wise" EXAMPLESDIR="share/examples/wise" DATADIR="share/wise" WWWDIR="www/wise" ETCDIR="etc/wise" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/wise DOCSDIR=/usr/local/share/doc/wise EXAMPLESDIR=/usr/local/share/examples/wise WWWDIR=/usr/local/www/wise ETCDIR=/usr/local/etc/wise --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 --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The wise port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> wise-2.4.1_1 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 ===> wise-2.4.1_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of wise-2.4.1_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The wise port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by wise-2.4.1_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The wise port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by wise-2.4.1_1 for building => SHA256 Checksum OK for wise2.4.1.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The wise port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by wise-2.4.1_1 for building ===> Extracting for wise-2.4.1_1 => SHA256 Checksum OK for wise2.4.1.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 wise-2.4.1_1 ===> Applying FreeBSD patches for wise-2.4.1_1 from /usr/ports/biology/wise/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> wise-2.4.1_1 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.4.3,1.pkg [pkg.DaveG.ca] Installing pkgconf-2.4.3,1... [pkg.DaveG.ca] Extracting pkgconf-2.4.3,1: .......... done ===> wise-2.4.1_1 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of wise-2.4.1_1 ===> wise-2.4.1_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> wise-2.4.1_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of wise-2.4.1_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> wise-2.4.1_1 depends on shared library: libglib-2.0.so - not found ===> Installing existing package /packages/All/glib-2.84.4,2.pkg [pkg.DaveG.ca] Installing glib-2.84.4,2... [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] `-- Installing libffi-3.5.1... [pkg.DaveG.ca] `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] `-- Installing libiconv-1.18_1... [pkg.DaveG.ca] `-- Extracting libiconv-1.18_1: .......... done [pkg.DaveG.ca] `-- Installing libinotify-20240724_3... [pkg.DaveG.ca] `-- Extracting libinotify-20240724_3: .......... done [pkg.DaveG.ca] `-- Installing pcre2-10.47_1... [pkg.DaveG.ca] `-- Extracting pcre2-10.47_1: .......... done [pkg.DaveG.ca] `-- Installing py311-packaging-25.0... [pkg.DaveG.ca] | `-- Installing python311-3.11.14... [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: .......... done [pkg.DaveG.ca] `-- Extracting py311-packaging-25.0: .......... done [pkg.DaveG.ca] Extracting glib-2.84.4,2: .......... done ==> 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 libinotify-20240724_3: -- You might want to consider increasing the kern.maxfiles tunable if you plan to use this library for applications that need to monitor activity of a lot of files. ===== Message from python311-3.11.14: -- 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 ===> wise-2.4.1_1 depends on shared library: libglib-2.0.so - found (/usr/local/lib/libglib-2.0.so) ===> Returning to build of wise-2.4.1_1 ===> wise-2.4.1_1 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for wise-2.4.1_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for wise-2.4.1_1 --- realall --- (cd base ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libwisebase.a ) --- wiseconfig.o --- --- wisestring.o --- --- wiseerror.o --- --- wisememman.o --- --- wisefile.o --- --- wiserandom.o --- --- wisetime.o --- --- wiseoverlay.o --- --- wisestreaminterface.o --- --- commandline.o --- --- linesubs.o --- --- wiseconfig.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wiseconfig.c --- wisestring.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wisestring.c --- wiseerror.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wiseerror.c --- wisememman.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wisememman.c --- wisefile.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wisefile.c --- wiserandom.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wiserandom.c --- wisetime.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wisetime.c --- commandline.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include commandline.c --- wiseoverlay.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wiseoverlay.c --- linesubs.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include linesubs.c --- wisestreaminterface.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include wisestreaminterface.c --- wisefile.o --- wisefile.dy:72:33: warning: format specifies type 'int' but the argument has type 'FILE *' (aka 'struct __sFILE *') [-Wformat] 72 | fprintf(stderr,"Closing %d\n",ofp); | ~~ ^~~ 1 warning generated. --- libwisebase.a --- ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o ar: warning: creating libwisebase.a if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi (cd HMMer2 ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libhmmer.a ) --- alphabet.o --- --- core_algorithms.o --- --- debug.o --- --- emit.o --- --- emulation.o --- --- histogram.o --- --- hmmio.o --- --- mathsupport.o --- --- masks.o --- --- misc.o --- --- modelmakers.o --- --- plan7.o --- --- plan9.o --- --- prior.o --- --- tophits.o --- --- trace.o --- --- aligneval.o --- --- alignio.o --- --- cluster.o --- --- dayhoff.o --- --- file.o --- --- getopt.o --- --- gnuregex.o --- --- interleaved.o --- --- iupac.o --- --- msf.o --- --- revcomp.o --- --- selex.o --- --- sqerror.o --- --- sqio.o --- --- sre_ctype.o --- --- sre_math.o --- --- sre_string.o --- --- stack.o --- --- translate.o --- --- types.o --- --- weight.o --- --- alphabet.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c alphabet.c --- core_algorithms.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c core_algorithms.c --- debug.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c debug.c --- emit.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c emit.c --- emulation.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c emulation.c --- histogram.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c histogram.c --- hmmio.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c hmmio.c --- mathsupport.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c mathsupport.c --- masks.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c masks.c --- misc.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c misc.c --- modelmakers.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c modelmakers.c --- plan7.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c plan7.c --- plan9.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c plan9.c --- prior.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c prior.c --- tophits.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c tophits.c --- trace.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c trace.c --- aligneval.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c aligneval.c --- alignio.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c alignio.c --- cluster.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c cluster.c --- dayhoff.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c dayhoff.c --- file.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c file.c --- getopt.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c getopt.c --- gnuregex.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c gnuregex.c --- interleaved.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c interleaved.c --- iupac.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c iupac.c --- msf.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c msf.c --- revcomp.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c revcomp.c --- selex.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c selex.c --- sqerror.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c sqerror.c --- sqio.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c sqio.c --- sre_ctype.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c sre_ctype.c --- sre_math.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c sre_math.c --- stack.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c stack.c --- translate.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c translate.c --- sre_string.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c sre_string.c --- types.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c types.c --- weight.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c weight.c --- alphabet.o --- alphabet.c:237:9: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses] 237 | if (! ainfo->sqinfo[idx].flags & SQINFO_LEN) { | ^ ~ alphabet.c:237:9: note: add parentheses after the '!' to evaluate the bitwise operator first 237 | if (! ainfo->sqinfo[idx].flags & SQINFO_LEN) { | ^ | ( ) alphabet.c:237:9: note: add parentheses around left hand side expression to silence this warning 237 | if (! ainfo->sqinfo[idx].flags & SQINFO_LEN) { | ^ | ( ) 1 warning generated. --- prior.o --- prior.c:102:12: warning: call to undeclared library function 'strcmp' with type 'int (const char *, const char *)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 102 | if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET; | ^ prior.c:102:12: note: include the header or explicitly provide a declaration for 'strcmp' 1 warning generated. --- interleaved.o --- interleaved.c:165:82: warning: size argument in 'strncmp' call is a comparison [-Wmemsize-comparison] 165 | if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) | ~~~~~~~~~~~~~~~~~~~~~~^~~~ interleaved.c:165:32: note: did you mean to compare the result of 'strncmp' instead? 165 | if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) | ^ ~ | ) interleaved.c:165:60: note: explicitly cast the argument to size_t to silence this warning 165 | if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) | ^ | (size_t)( ) interleaved.c:240:82: warning: size argument in 'strncmp' call is a comparison [-Wmemsize-comparison] 240 | if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) | ~~~~~~~~~~~~~~~~~~~~~~^~~~ interleaved.c:240:32: note: did you mean to compare the result of 'strncmp' instead? 240 | if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) | ^ ~ | ) interleaved.c:240:60: note: explicitly cast the argument to size_t to silence this warning 240 | if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) | ^ | (size_t)( ) 2 warnings generated. --- sqio.o --- sqio.c:1033:9: warning: comparison of array 'sp' equal to a null pointer is always false [-Wtautological-pointer-compare] 1033 | if (sp==NULL || *sp=='\0') | ^~ ~~~~ 1 warning generated. --- gnuregex.o --- gnuregex.c:795:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 795 | re_set_syntax (syntax) | ^ gnuregex.c:1175:37: warning: passing arguments to 'at_begline_loc_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1175 | || at_begline_loc_p (pattern, p, syntax)) | ^ gnuregex.c:1190:37: warning: passing arguments to 'at_endline_loc_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1190 | || at_endline_loc_p (p, pend, syntax)) | ^ gnuregex.c:1296:21: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1296 | STORE_JUMP (jump, b, laststart); | ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' 903 | store_op1 (op, loc, (to) - (loc) - 3) | ^ gnuregex.c:1301:19: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1301 | STORE_JUMP (maybe_pop_jump, b, laststart - 3); | ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' 903 | store_op1 (op, loc, (to) - (loc) - 3) | ^ gnuregex.c:1310:13: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1310 | INSERT_JUMP (keep_string_p ? on_failure_keep_string_jump | ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' 911 | insert_op1 (op, loc, (to) - (loc) - 3, b) | ^ gnuregex.c:1324:17: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1324 | INSERT_JUMP (dummy_failure_jump, laststart, laststart + 6); | ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' 911 | insert_op1 (op, loc, (to) - (loc) - 3, b) | ^ gnuregex.c:1407:39: warning: passing arguments to 'compile_range' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1407 | = compile_range (&p, pend, translate, syntax, b); | ^ gnuregex.c:1418:41: warning: passing arguments to 'compile_range' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1418 | ret = compile_range (&p, pend, translate, syntax, b); | ^ gnuregex.c:1616:17: warning: add explicit braces to avoid dangling else [-Wdangling-else] 1616 | else | ^ gnuregex.c:1629:19: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1629 | STORE_JUMP (jump_past_alt, fixup_alt_jump, b - 1); | ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' 903 | store_op1 (op, loc, (to) - (loc) - 3) | ^ gnuregex.c:1636:17: warning: add explicit braces to avoid dangling else [-Wdangling-else] 1636 | else | ^ gnuregex.c:1686:15: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1686 | INSERT_JUMP (on_failure_jump, begalt, b + 6); | ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' 911 | insert_op1 (op, loc, (to) - (loc) - 3, b) | ^ gnuregex.c:1707:17: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1707 | STORE_JUMP (jump_past_alt, fixup_alt_jump, b); | ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' 903 | store_op1 (op, loc, (to) - (loc) - 3) | ^ gnuregex.c:1801:22: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1801 | INSERT_JUMP (jump, laststart, b + 3); | ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' 911 | insert_op1 (op, loc, (to) - (loc) - 3, b) | ^ gnuregex.c:1826:22: warning: passing arguments to 'insert_op2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1826 | INSERT_JUMP2 (succeed_n, laststart, | ^ gnuregex.c:915:14: note: expanded from macro 'INSERT_JUMP2' 915 | insert_op2 (op, loc, (to) - (loc) - 3, arg, b) | ^ gnuregex.c:1835:33: warning: passing arguments to 'insert_op2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1835 | insert_op2 (set_number_at, laststart, 5, lower_bound, b); | ^ gnuregex.c:1846:26: warning: passing arguments to 'store_op2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1846 | STORE_JUMP2 (jump_n, b, laststart + 5, | ^ gnuregex.c:907:13: note: expanded from macro 'STORE_JUMP2' 907 | store_op2 (op, loc, (to) - (loc) - 3, arg) | ^ gnuregex.c:1864:37: warning: passing arguments to 'insert_op2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1864 | insert_op2 (set_number_at, laststart, b - laststart, | ^ gnuregex.c:1958:42: warning: passing arguments to 'group_in_compile_stack' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1958 | if (group_in_compile_stack (compile_stack, c1)) | ^ gnuregex.c:2024:5: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2024 | STORE_JUMP (jump_past_alt, fixup_alt_jump, b); | ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' 903 | store_op1 (op, loc, (to) - (loc) - 3) | ^ gnuregex.c:1049:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1049 | regex_compile (pattern, size, syntax, bufp) | ^ gnuregex.c:2050:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2050 | store_op1 (op, loc, arg) | ^ gnuregex.c:829:13: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 829 | static void store_op1 (), store_op2 (); | ^ gnuregex.c:2063:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2063 | store_op2 (op, loc, arg1, arg2) | ^ gnuregex.c:829:27: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 829 | static void store_op1 (), store_op2 (); | ^ gnuregex.c:2078:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2078 | insert_op1 (op, loc, arg, end) | ^ gnuregex.c:830:13: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 830 | static void insert_op1 (), insert_op2 (); | ^ gnuregex.c:2097:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2097 | insert_op2 (op, loc, arg1, arg2, end) | ^ gnuregex.c:830:28: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 830 | static void insert_op1 (), insert_op2 (); | ^ gnuregex.c:2118:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2118 | at_begline_loc_p (pattern, p, syntax) | ^ gnuregex.c:831:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 831 | static boolean at_begline_loc_p (), at_endline_loc_p (); | ^ gnuregex.c:2137:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2137 | at_endline_loc_p (p, pend, syntax) | ^ gnuregex.c:831:37: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 831 | static boolean at_begline_loc_p (), at_endline_loc_p (); | ^ gnuregex.c:2159:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2159 | group_in_compile_stack (compile_stack, regnum) | ^ gnuregex.c:832:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 832 | static boolean group_in_compile_stack (); | ^ gnuregex.c:2187:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2187 | compile_range (p_ptr, pend, translate, syntax, b) | ^ gnuregex.c:833:22: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 833 | static reg_errcode_t compile_range (); | ^ gnuregex.c:2519:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2519 | re_compile_fastmap (bufp) | ^ gnuregex.c:2804:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2804 | re_set_registers (bufp, regs, num_regs, starts, ends) | ^ gnuregex.c:2821:33: warning: expression which evaluates to zero treated as a null pointer constant of type 'regoff_t *' (aka 'int *') [-Wnon-literal-null-conversion] 2821 | regs->start = regs->end = (regoff_t) 0; | ^~~~~~~~~~~~ gnuregex.c:2831:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2831 | re_search (bufp, string, size, startpos, range, regs) | ^ gnuregex.c:2864:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2864 | re_search_2 (bufp, string1, size1, string2, size2, startpos, range, regs, stop) | ^ gnuregex.c:3123:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3123 | re_match (bufp, string, size, pos, regs) | ^ gnuregex.c:3148:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3148 | re_match_2 (bufp, string1, size1, string2, size2, pos, regs, stop) | ^ gnuregex.c:3604:43: warning: passing arguments to 'group_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3604 | = group_match_null_string_p (&p1, pend, reg_info); | ^ gnuregex.c:3752:31: warning: cast to smaller integer type 'int' from 'char *' [-Wpointer-to-int-cast] 3752 | if ((int) old_regend[r] >= (int) regstart[r]) | ^~~~~~~~~~~~~~~~~~~ gnuregex.c:3752:54: warning: cast to smaller integer type 'int' from 'char *' [-Wpointer-to-int-cast] 3752 | if ((int) old_regend[r] >= (int) regstart[r]) | ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3822:38: warning: passing arguments to 'bcmp_translate' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3822 | ? bcmp_translate (d, d2, mcnt, translate) | ^ gnuregex.c:3905:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4064:13: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] 4064 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4065 | dummy_low_reg, dummy_high_reg, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4066 | reg_dummy, reg_dummy, reg_info_dummy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: note: expanded from macro 'POP_FAILURE_POINT' 2482 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4064:13: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] 4064 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4065 | dummy_low_reg, dummy_high_reg, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4066 | reg_dummy, reg_dummy, reg_info_dummy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: note: expanded from macro 'POP_FAILURE_POINT' 2485 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4278:11: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] 4278 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~~~~~~~~ 4279 | lowest_active_reg, highest_active_reg, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4280 | regstart, regend, reg_info); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: note: expanded from macro 'POP_FAILURE_POINT' 2482 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4278:11: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] 4278 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~~~~~~~~ 4279 | lowest_active_reg, highest_active_reg, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4280 | regstart, regend, reg_info); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: note: expanded from macro 'POP_FAILURE_POINT' 2485 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4394:48: warning: passing arguments to 'alt_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4394 | if (!alt_match_null_string_p (p1, p1 + mcnt - 3, | ^ gnuregex.c:4424:44: warning: passing arguments to 'alt_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4424 | if (!alt_match_null_string_p (p1, p1 + mcnt, reg_info)) | ^ gnuregex.c:4439:46: warning: passing arguments to 'common_op_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4439 | if (!common_op_match_null_string_p (&p1, end, reg_info)) | ^ gnuregex.c:4344:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4344 | group_match_null_string_p (p, end, reg_info) | ^ gnuregex.c:2984:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 2984 | group_match_null_string_p (); | ^ gnuregex.c:4475:46: warning: passing arguments to 'common_op_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4475 | if (!common_op_match_null_string_p (&p1, end, reg_info)) | ^ gnuregex.c:4453:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4453 | alt_match_null_string_p (p, end, reg_info) | ^ gnuregex.c:2982:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 2982 | static boolean alt_match_null_string_p (), | ^ gnuregex.c:4490:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4490 | common_op_match_null_string_p (p, end, reg_info) | ^ gnuregex.c:2983:16: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 2983 | common_op_match_null_string_p (), | ^ gnuregex.c:4578:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4578 | bcmp_translate (s1, s2, len, translate) | ^ gnuregex.c:2981:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent definition [-Wdeprecated-non-prototype] 2981 | static int bcmp_translate (); | ^ gnuregex.c:4634:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4634 | re_comp (s) | ^ gnuregex.c:4672:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4672 | re_exec (s) | ^ gnuregex.c:4720:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4720 | regcomp (preg, pattern, cflags) | ^ gnuregex.c:4795:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4795 | regexec (preg, string, nmatch, pmatch, eflags) | ^ gnuregex.c:4860:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4860 | regerror (errcode, preg, errbuf, errbuf_size) | ^ gnuregex.c:4904:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 4904 | regfree (preg) | ^ 81 warnings generated. --- libhmmer.a --- ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o a - alphabet.o a - core_algorithms.o a - debug.o a - emit.o a - emulation.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - prior.o a - tophits.o a - trace.o a - aligneval.o a - alignio.o a - cluster.o a - dayhoff.o a - file.o a - getopt.o a - gnuregex.o a - interleaved.o a - iupac.o a - msf.o a - revcomp.o a - selex.o a - sqerror.o a - sqio.o a - sre_ctype.o a - sre_math.o a - sre_string.o a - stack.o a - translate.o a - types.o a - weight.o if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libdyna.a ) --- packaln.o --- --- aln.o --- --- dnamatrix.o --- --- probability.o --- --- alnrange.o --- --- alnconvert.o --- --- basematrix.o --- --- shattermatrix.o --- --- matrixdebug.o --- --- dpenvelope.o --- --- dbsearchimpl.o --- --- dprunimpl.o --- --- complexsequence.o --- --- complexevalset.o --- --- complexconsensi.o --- --- sequence.o --- --- sequencestream.o --- --- seqalign.o --- --- hitlist.o --- --- hsp.o --- --- hspstream.o --- --- codon.o --- --- compmat.o --- --- codonmatrix.o --- --- codonmapper.o --- --- sequencedb.o --- --- hscore.o --- --- seqlookup.o --- --- arrayseqlookup.o --- --- genericindexresult.o --- --- linkedlist_lookpos.o --- --- singlenumberspace.o --- --- histogram.o --- --- searchstatinterface.o --- --- searchstatlookup.o --- --- proteindb.o --- --- protein.o --- --- pairbase.o --- --- pairbaseseq.o --- --- genomicdb.o --- --- randommodel.o --- --- randomdb.o --- --- genomic.o --- --- cdna.o --- --- cdnadb.o --- --- dna.o --- --- embl.o --- --- genomicregion.o --- --- gene.o --- --- transcript.o --- --- translation.o --- --- btcanvas.o --- --- asciibtcanvas.o --- --- dynlibcross.o --- --- packaln.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ packaln.c --- aln.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ aln.c --- dnamatrix.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ dnamatrix.c --- probability.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ probability.c --- alnrange.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ alnrange.c --- alnconvert.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ alnconvert.c --- basematrix.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ basematrix.c --- shattermatrix.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ shattermatrix.c --- matrixdebug.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ matrixdebug.c --- dpenvelope.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ dpenvelope.c --- dbsearchimpl.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ dbsearchimpl.c --- dprunimpl.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ dprunimpl.c --- complexsequence.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ complexsequence.c --- complexevalset.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ complexevalset.c --- complexconsensi.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ complexconsensi.c --- sequence.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ sequence.c --- sequencestream.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ sequencestream.c --- seqalign.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ seqalign.c --- hitlist.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hitlist.c --- hsp.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsp.c --- hspstream.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hspstream.c --- codon.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ codon.c --- compmat.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ compmat.c --- codonmatrix.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ codonmatrix.c --- codonmapper.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ codonmapper.c --- sequencedb.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ sequencedb.c --- hscore.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hscore.c --- seqlookup.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ seqlookup.c --- arrayseqlookup.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ arrayseqlookup.c --- genericindexresult.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ genericindexresult.c --- linkedlist_lookpos.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ linkedlist_lookpos.c --- singlenumberspace.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ singlenumberspace.c --- histogram.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ histogram.c --- searchstatinterface.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ searchstatinterface.c --- searchstatlookup.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ searchstatlookup.c --- proteindb.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ proteindb.c --- protein.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ protein.c --- pairbase.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ pairbase.c --- pairbaseseq.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ pairbaseseq.c --- genomicdb.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ genomicdb.c --- randommodel.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ randommodel.c --- randomdb.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ randomdb.c --- genomic.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ genomic.c --- cdna.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ cdna.c --- cdnadb.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ cdnadb.c --- dna.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ dna.c --- embl.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ embl.c --- genomicregion.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ genomicregion.c --- gene.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ gene.c --- transcript.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ transcript.c --- translation.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ translation.c --- btcanvas.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ btcanvas.c --- asciibtcanvas.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ asciibtcanvas.c --- dynlibcross.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ dynlibcross.c --- dpenvelope.o --- dpenvelope.dy:68:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] 68 | } | ^ 1 warning generated. --- aln.o --- aln.dy:867:65: warning: data argument not used by format string [-Wformat-extra-args] 867 | fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml); | ~~~~~~~~~~~~ ^ 1 warning generated. --- libdyna.a --- ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o ar: warning: creating libdyna.a if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libdyna_glib.a ) --- subseqhash.o --- --- intallocator.o --- --- proteinstreamedindex.o --- --- shadowseq.o --- --- shadowseqindex.o --- --- hsphandler.o --- --- hspscaninterface.o --- --- hsp2hitscan.o --- --- hsplookupscan.o --- --- hsplookupthreaded.o --- --- hspthreadeddb.o --- --- hspscanruntime.o --- --- hsptwohitscan.o --- --- proteinindexcons.o --- --- dnaindexcons.o --- --- staticseq.o --- --- subseqhash.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ subseqhash.c --- intallocator.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ intallocator.c --- proteinstreamedindex.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ proteinstreamedindex.c --- shadowseq.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ shadowseq.c --- shadowseqindex.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ shadowseqindex.c --- hsphandler.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsphandler.c --- hspscaninterface.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hspscaninterface.c --- hsp2hitscan.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsp2hitscan.c --- hsplookupscan.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsplookupscan.c --- hspthreadeddb.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hspthreadeddb.c --- hsplookupthreaded.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsplookupthreaded.c --- hsptwohitscan.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsptwohitscan.c --- proteinindexcons.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ proteinindexcons.c --- hspscanruntime.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hspscanruntime.c --- dnaindexcons.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ dnaindexcons.c --- staticseq.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ staticseq.c --- subseqhash.o --- subseqhash.dy:111:29: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] 111 | if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ subseqhash.dy:128:85: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] 128 | return new_linkedl_SeqLookupResultInterface((SeqLookupPos *)g_hash_table_lookup(h,(gconstpointer)seq_number)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ subseqhash.dy:160:54: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] 160 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ subseqhash.dy:161:29: warning: cast to 'gpointer' (aka 'void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] 161 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^~~~~~~~~~~~~~~~~~~~ subseqhash.dy:188:52: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] 188 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ subseqhash.dy:189:27: warning: cast to 'gpointer' (aka 'void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] 189 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^~~~~~~~~~~~~~~~~~~~ 6 warnings generated. --- hspthreadeddb.o --- hspthreadeddb.dy:154:77: warning: cast to smaller integer type 'int' from 'Wise2_LinearHSPmanager *' (aka 'struct Wise2_LinearHSPmanager *') [-Wpointer-to-int-cast] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ^~~~~~~~~~~~ hspthreadeddb.dy:154:73: warning: format specifies type 'int' but the argument has type 'Wise2_HSPDatabaseSegment *' (aka 'struct Wise2_HSPDatabaseSegment *') [-Wformat] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ~~ ^~~ 2 warnings generated. --- shadowseqindex.o --- shadowseqindex.dy:285:59: warning: format specifies type 'double' but the argument has type 'unsigned long' [-Wformat] 285 | fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); | ~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | %.2lu 1 warning generated. --- hsplookupthreaded.o --- hsplookupthreaded.dy:263:55: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] 263 | fprintf(stderr,"retrieved array with %d elements\n",current_oph); | ~~ ^~~~~~~~~~~ | %ld hsplookupthreaded.dy:567:1: warning: non-void function does not return a value [-Wreturn-type] 567 | } | ^ 2 warnings generated. --- hsp2hitscan.o --- hsp2hitscan.dy:210:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ~~ | %ld 210 | use.ru_utime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:211:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ~~~~ | %03ld 210 | use.ru_utime.tv_sec, 211 | use.ru_utime.tv_sec/1000, | ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:212:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ~~ | %ld 210 | use.ru_utime.tv_sec, 211 | use.ru_utime.tv_sec/1000, 212 | use.ru_stime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:213:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ~~~~ | %03ld 210 | use.ru_utime.tv_sec, 211 | use.ru_utime.tv_sec/1000, 212 | use.ru_stime.tv_sec, 213 | use.ru_stime.tv_sec/1000 | ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:274:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ~~ | %ld 274 | use.ru_utime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:275:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ~~~~ | %03ld 274 | use.ru_utime.tv_sec, 275 | use.ru_utime.tv_sec/1000, | ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:276:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ~~ | %ld 274 | use.ru_utime.tv_sec, 275 | use.ru_utime.tv_sec/1000, 276 | use.ru_stime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:277:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ~~~~ | %03ld 274 | use.ru_utime.tv_sec, 275 | use.ru_utime.tv_sec/1000, 276 | use.ru_stime.tv_sec, 277 | use.ru_stime.tv_sec/1000 | ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:287:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ~~ | %ld 287 | use.ru_utime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:288:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ~~~~ | %03ld 287 | use.ru_utime.tv_sec, 288 | use.ru_utime.tv_sec/1000, | ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:289:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ~~ | %ld 287 | use.ru_utime.tv_sec, 288 | use.ru_utime.tv_sec/1000, 289 | use.ru_stime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:290:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ~~~~ | %03ld 287 | use.ru_utime.tv_sec, 288 | use.ru_utime.tv_sec/1000, 289 | use.ru_stime.tv_sec, 290 | use.ru_stime.tv_sec/1000 | ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:303:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ~~ | %ld 303 | use.ru_utime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:304:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ~~~~ | %03ld 303 | use.ru_utime.tv_sec, 304 | use.ru_utime.tv_sec/1000, | ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:305:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ~~ | %ld 303 | use.ru_utime.tv_sec, 304 | use.ru_utime.tv_sec/1000, 305 | use.ru_stime.tv_sec, | ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:306:4: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ~~~~ | %03ld 303 | use.ru_utime.tv_sec, 304 | use.ru_utime.tv_sec/1000, 305 | use.ru_stime.tv_sec, 306 | use.ru_stime.tv_sec/1000 | ^~~~~~~~~~~~~~~~~~~~~~~~ 16 warnings generated. --- libdyna_glib.a --- ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: warning: creating libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi (cd external ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" all ) --- all --- (cd mott; make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include" all) --- mott_api.o --- --- gaplib.o --- --- wise2_mott_bridge.o --- --- mott_api.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c mott_api.c -o mott_api.o --- gaplib.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c gaplib.c -o gaplib.o --- wise2_mott_bridge.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../../dynlibsrc -I../../base wise2_mott_bridge.c --- mott_api.o --- mott_api.c:64:3: warning: call to undeclared library function 'free' with type 'void (void *)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 64 | free(freq0); | ^ mott_api.c:64:3: note: include the header or explicitly provide a declaration for 'free' mott_api.c:179:16: warning: call to undeclared library function 'calloc' with type 'void *(unsigned long, unsigned long)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 179 | h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin; | ^ mott_api.c:179:16: note: include the header or explicitly provide a declaration for 'calloc' mott_api.c:207:12: warning: call to undeclared library function 'toupper' with type 'int (int)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 207 | freq[toupper(seq[n])]++; | ^ mott_api.c:207:12: note: include the header or explicitly provide a declaration for 'toupper' 3 warnings generated. --- libmott.a --- ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: warning: creating libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi (cd socket ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libwisesocket.a ) --- functionserver.o --- --- functionclient.o --- --- anonobj.o --- --- transferinterface.o --- --- directsocketwrite.o --- --- functionserver.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ functionserver.c --- functionclient.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ functionclient.c --- anonobj.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ anonobj.c --- directsocketwrite.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ directsocketwrite.c --- transferinterface.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ transferinterface.c --- functionclient.o --- functionclient.dy:193:24: warning: incompatible pointer types passing 'struct sockaddr_in *' to parameter of type 'const struct sockaddr *' [-Wincompatible-pointer-types] 193 | connect(out->socket, &server, sizeof(server)); | ^~~~~~~ /usr/include/sys/socket.h:683:41: note: passing argument to parameter here 683 | int connect(int, const struct sockaddr *, socklen_t); | ^ 1 warning generated. --- libwisesocket.a --- ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: warning: creating libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi (cd dnaindex ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" all ) --- kmer_assembly.o --- --- kmer_index_interface.o --- --- kmer_direct.o --- --- kmer_hash.o --- --- kmer_count.o --- --- kmer_glib_index.o --- --- singleseqspace.o --- --- dnamapping.o --- --- largeseqreader.o --- --- kmer_assembly_untangler.o --- --- kmer_assembly_contig.o --- --- kmer_assembly_error.o --- --- assembly.o --- --- assembly_stream_interface.o --- --- assembly_stream_fasta.o --- --- assembly_sanger_project.o --- --- assembly_stream_cons.o --- --- compressed_protein_index.o --- --- kmer_assembly.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c --- kmer_index_interface.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c --- kmer_direct.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c --- kmer_hash.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c --- kmer_count.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c --- kmer_glib_index.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c --- singleseqspace.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c --- dnamapping.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c --- largeseqreader.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c --- kmer_assembly_untangler.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c --- kmer_assembly_contig.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c --- assembly.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly.c --- assembly_stream_interface.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c --- kmer_assembly_error.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c --- assembly_stream_fasta.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c --- assembly_sanger_project.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c --- assembly_stream_cons.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c --- compressed_protein_index.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c --- kmer_hash.o --- kmer_hash.dy:318:41: warning: format specifies type 'unsigned long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 318 | fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer); | ~~~~~~ ^~~~~~~~~~~~~ | %016llx kmer_hash.dy:319:41: warning: format specifies type 'unsigned long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 319 | fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer); | ~~~~~~ ^~~~~~~~~~~~~ | %016llx 2 warnings generated. --- kmer_assembly.o --- kmer_assembly.dy:296:44: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 296 | fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer); | ~~~ ^~~~~~~~~~~~ | %lld kmer_assembly.dy:302:104: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 302 | fprintf(ofp," ... prev ... %c, %d to %ld\n",node->prev[i]->base,node->prev[i]->sequence_label_len,node->prev[i]->prev->number); | ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ | %lld kmer_assembly.dy:309:104: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 309 | fprintf(ofp," ... next ... %c, %d to %ld\n",node->next[i]->base,node->next[i]->sequence_label_len,node->next[i]->next->number); | ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ | %lld kmer_assembly.dy:365:88: warning: format specifies type 'long' but the argument has type 'KmerAssemblyLink *' (aka 'struct KmerAssemblyLink *') [-Wformat] 365 | fprintf(stderr," ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len); | ~~~ ^~~ kmer_assembly.dy:367:36: warning: more '%' conversions than data arguments [-Wformat-insufficient-args] 367 | fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); | ~^ 5 warnings generated. --- compressed_protein_index.o --- compressed_protein_index.dy:223:10: warning: incompatible pointer to integer conversion returning 'void *' from a function with result type 'boolean' (aka 'int') [-Wint-conversion] 223 | return NULL; | ^~~~ /usr/include/sys/_null.h:32:14: note: expanded from macro 'NULL' 32 | #define NULL ((void *)0) | ^~~~~~~~~~~ 1 warning generated. --- kmer_assembly_untangler.o --- kmer_assembly_untangler.dy:52:65: warning: cast to smaller integer type 'int' from 'KmerAssemblyLink *' (aka 'struct KmerAssemblyLink *') [-Wpointer-to-int-cast] 52 | fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base); | ^~~~~~~~~~~~~~~~~~ kmer_assembly_untangler.dy:120:80: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 120 | fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); | ~~~ ^~~~~~~~~~~~ | %lld kmer_assembly_untangler.dy:141:71: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ | %lld kmer_assembly_untangler.dy:141:99: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ~~~ ^~~~~~~~~~~~ | %lld kmer_assembly_untangler.dy:157:73: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 157 | fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer); | ~~~ ^~~~~~~~~~~~ | %lld kmer_assembly_untangler.dy:159:69: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 159 | fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer); | ~~~ ^~~~~~~~~~~~ | %lld kmer_assembly_untangler.dy:444:89: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 444 | fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len); | ~~~ ^~~~~~~~~~~~~~~~~~~~~ | %lld kmer_assembly_untangler.dy:568:75: warning: incompatible pointer types passing 'long[10000]' to parameter of type 'int *' [-Wincompatible-pointer-types] 568 | lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); | ^~~~~~~~~~~~~~~~~ ./kmer_assembly_untangler.h:174:116: note: passing argument to parameter 'start_label' here 174 | void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len); | ^ kmer_assembly_untangler.dy:746:149: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 746 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ | %lld kmer_assembly_untangler.dy:746:182: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 746 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ | %lld 10 warnings generated. --- kmer_assembly_error.o --- kmer_assembly_error.dy:93:66: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 93 | fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer); | ~~~ ^~~~~~~~~~~~ | %lld kmer_assembly_error.dy:105:66: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat] 105 | fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer); | ~~~ ^~~~~~~~~~~~ | %lld kmer_assembly_error.dy:351:127: warning: format specifies type 'int' but the argument has type 'int *' [-Wformat] 351 | fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos); | ~~ ^~~~~~~~~~~~ 3 warnings generated. (cd network ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" all ) --- wise_proteinindex_server.o --- --- net_hspscan.o --- --- client_multihspscan.o --- --- wise_proteinindex_server.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c --- client_multihspscan.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c --- net_hspscan.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c --- client_multihspscan.o --- client_multihspscan.dy:128:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] 128 | } | ^ 1 warning generated. --- scanwise_server --- cc -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs` -pthread (cd models ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) --- dnal.o --- --- psw.o --- --- pswdb.o --- --- dbac.o --- --- estwise.o --- --- genewise.o --- --- genewisedb.o --- --- estwisedb.o --- --- genomewise.o --- --- sywise.o --- --- pseudowise.o --- --- promoterwise.o --- --- scanwisep_wiseserver.o --- --- dnaalign.o --- --- seqaligndisplay.o --- --- proteinsw.o --- --- sw_wrap.o --- --- abc.o --- --- pba.o --- --- dba.o --- --- slimdba.o --- --- bigdba.o --- --- dbadisplay.o --- --- geneparser21.o --- --- geneparameter.o --- --- genestats.o --- --- genewisehsp.o --- --- geneutil.o --- --- geneoutput.o --- --- threestatemodel.o --- --- genefrequency.o --- --- splicesitemodeler.o --- --- genewise4.o --- --- genewise6.o --- --- genestretch6.o --- --- genewise21.o --- --- geneloop21.o --- --- geneloop6.o --- --- genephase6.o --- --- gwlite.o --- --- gwlitemodel.o --- --- gwrap.o --- --- matchsum.o --- --- estwrap.o --- --- genewisemodel.o --- --- phasemodel.o --- --- cdparser.o --- --- genedisplay.o --- --- estwise3.o --- --- estslim3.o --- --- estloop3.o --- --- estfrag3.o --- --- estslimloop.o --- --- gwquickdb.o --- --- threestatedb.o --- --- pfamhmmer1db.o --- --- pwmdna.o --- --- wise2xhmmer2.o --- --- genewisemodeldb.o --- --- seqhit.o --- --- standardout.o --- --- geneparser4.o --- --- estquick3.o --- --- genomewise9.o --- --- cdparser.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ cdparser.c --- estwrap.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ estwrap.c --- gwlitemodel.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ gwlitemodel.c --- splicesitemodeler.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c --- geneoutput.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ geneoutput.c --- geneparser21.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ geneparser21.c --- dbadisplay.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ dbadisplay.c --- sw_wrap.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ sw_wrap.c --- seqaligndisplay.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ seqaligndisplay.c --- pseudowise.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ pseudowise.c --- sywise.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ sywise.c --- genomewise.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genomewise.c --- dbac.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ dbac.c dbac.c:413:45: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] 413 | fprintf(stderr,"Got %d with %d vs %d\n",i,strlen(seq),one->len); | ~~ ^~~~~~~~~~~ | %lu 1 warning generated. --- pswdb.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ pswdb.c --- psw.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ psw.c --- dnal.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ dnal.c --- estwise3.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ estwise3.c --- estslim3.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ estslim3.c --- estloop3.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ estloop3.c --- estfrag3.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ estfrag3.c --- estwise.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. --- genewise.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. --- genewisedb.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ --- estwisedb.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ --- estslimloop.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ estslimloop.c --- gwquickdb.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ gwquickdb.c --- threestatedb.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ threestatedb.c --- promoterwise.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` promoterwise.c --- scanwisep_wiseserver.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c --- dnaalign.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ dnaalign.c --- pfamhmmer1db.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ pfamhmmer1db.c --- proteinsw.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ proteinsw.c --- pwmdna.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ pwmdna.c --- abc.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ abc.c --- pba.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ pba.c --- dba.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ dba.c --- slimdba.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ slimdba.c --- bigdba.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ bigdba.c --- wise2xhmmer2.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c --- genewisemodeldb.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genewisemodeldb.c --- geneparameter.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ geneparameter.c --- genestats.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genestats.c --- genewisehsp.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genewisehsp.c --- geneutil.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ geneutil.c --- seqhit.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ seqhit.c --- threestatemodel.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ threestatemodel.c --- genefrequency.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genefrequency.c --- standardout.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ standardout.c --- genewise4.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genewise4.c --- genewise6.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genewise6.c --- genestretch6.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genestretch6.c --- genewise21.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genewise21.c --- geneloop21.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ geneloop21.c --- geneloop6.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ geneloop6.c --- genephase6.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genephase6.c --- gwlite.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ gwlite.c --- geneparser4.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ geneparser4.c --- gwrap.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ gwrap.c --- matchsum.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ matchsum.c --- estquick3.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ estquick3.c --- genewisemodel.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genewisemodel.c --- phasemodel.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ phasemodel.c --- genomewise9.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genomewise9.c --- genedisplay.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genedisplay.c --- genome_evidence.o --- --- est_evidence.o --- --- sywise20.o --- --- syexonmodel.o --- --- pseudowise7.o --- --- localdba.o --- --- localcishit.o --- --- localcispara.o --- --- motifmatrix.o --- --- motifmatrixdp.o --- --- transfactor.o --- --- pairwiseshortdna.o --- --- hsp2aln_sw.o --- --- gwquickdb.o --- gwquickdb.dy:46:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] 46 | } | ^ gwquickdb.dy:65:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] 65 | } | ^ 2 warnings generated. --- genome_evidence.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ genome_evidence.c --- est_evidence.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ est_evidence.c --- motifmatrix.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ motifmatrix.c --- motifmatrixdp.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ motifmatrixdp.c --- sywise20.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ sywise20.c --- transfactor.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ transfactor.c --- syexonmodel.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ syexonmodel.c --- pseudowise7.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ pseudowise7.c --- localdba.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ localdba.c --- localcishit.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` localcishit.c --- localcispara.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ localcispara.c --- hsp2aln_sw.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` hsp2aln_sw.c --- genedisplay.o --- genedisplay.dy:493:37: warning: data argument not used by format string [-Wformat-extra-args] 493 | sprintf(buffer," Intron ??? ",in_number); | ~~~~~~~~~~~~~~~~ ^ 1 warning generated. --- pairwiseshortdna.o --- cc -O2 -pipe -Wno-error=int-conversion -Wno-error=incompatible-function-pointer-types -fstack-protector-strong -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ pairwiseshortdna.c --- genome_evidence.o --- genome_evidence.dy:61:1: warning: non-void function does not return a value [-Wreturn-type] 61 | } | ^ 1 warning generated. --- est_evidence.o --- est_evidence.dy:142:16: warning: incompatible function pointer types assigning to 'int (*)(void *)' from 'Wise2_EstEvidence *(Wise2_EstEvidence *)' (aka 'struct Wise2_EstEvidence *(struct Wise2_EstEvidence *)') [-Wincompatible-function-pointer-types] 142 | in->geu_free = free_EstEvidence; | ^ ~~~~~~~~~~~~~~~~ 1 warning generated. --- motifmatrix.o --- motifmatrix.c:408:24: warning: incompatible pointer to integer conversion assigning to 'char' from 'void *' [-Wint-conversion] 408 | out->mat[i][j] = NULL; | ^ ~~~~ 1 warning generated. --- dnal --- cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm --- psw --- --- scanwise --- --- pswdb --- --- psw --- cc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm --- scanwise --- cc -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -pthread --- pswdb --- cc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm --- transfactor.o --- transfactor.dy:339:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] 339 | } | ^ 1 warning generated. --- dba --- cc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm --- promoterwise --- cc -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` -pthread --- genephase6.o --- genephase6.c:873:1: warning: non-void function does not return a value [-Wreturn-type] 873 | } | ^ 1 warning generated. --- genomewise9.o --- genomewise9.c:745:1: warning: non-void function does not return a value [-Wreturn-type] 745 | } | ^ 1 warning generated. --- genomewise --- cc -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm --- sywise20.o --- sywise20.c:764:1: warning: non-void function does not return a value [-Wreturn-type] 764 | } | ^ 1 warning generated. --- sywise --- cc -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm --- libmodel.a --- --- genewise --- --- genewisedb --- --- estwisedb --- --- estwise --- --- pseudowise --- --- libmodel.a --- ar ru libmodel.a geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o --- genewise --- cc -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm --- genewisedb --- cc -o genewisedb genewisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm --- estwisedb --- cc -o estwisedb estwisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm --- estwise --- cc -o estwise estwise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm --- pseudowise --- cc -o pseudowise pseudowise.o pseudowise7.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm --- libmodel.a --- ar: warning: creating libmodel.a --- all --- /usr/bin/make bin --- bin --- mkdir bin cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for wise-2.4.1_1 ===> Generating temporary packing list (cd /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/src/bin && install -s -m 555 dba dnal estwise estwisedb genewise genewisedb promoterwise psw pswdb scanwise scanwise_server /wrkdirs/usr/ports/biology/wise/work/stage/usr/local/bin) (cd /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/wisecfg && install -m 0644 BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla aa.rnd cb.tmf codon.table gene.stat gon120.bla gon160.bla gon200.bla gon250.bla gon350.bla human.gf human.gp human.stats idenity.bla methods pb.gf pombe.gf tm.pri wise.2 wise.per worm.gf /wrkdirs/usr/ports/biology/wise/work/stage/usr/local/share/wise) (cd /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/docs && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /wrkdirs/usr/ports/biology/wise/work/stage/usr/local/share/doc/wise) (cd /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/test_data && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /wrkdirs/usr/ports/biology/wise/work/stage/usr/local/share/examples/wise) ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-01-25T12:14:29+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=4485bd8221c2' '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 wise-2.4.1_1 ===> Building wise-2.4.1_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for wise-2.4.1_1 build of biology/wise | wise-2.4.1_1 ended at Sun Jan 25 07:14:53 EST 2026 build time: 00:00:25