=>> Building biology/fasta3 build started at Wed Dec 10 23:59:48 EST 2025 port directory: /usr/ports/biology/fasta3 package name: fasta3-36.3.8_1 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: wendell@bsd.com.br Makefile datestamp: -rw-r--r-- 1 root wheel 2348 Aug 27 2024 /usr/ports/biology/fasta3/Makefile Ports top last git commit: 62d8b1999233 Ports top unclean checkout: no Port dir last git commit: 1b819e486953 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1305000 Job Id: 14 ---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/14/.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 fasta3-36.3.8_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-- wendell@bsd.com.br --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fasta3/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fasta3/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fasta3/work/.cache HOME=/wrkdirs/usr/ports/biology/fasta3/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fasta3/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fasta3/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-- THR_LIBS="-pthread" XDIR="/wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/bin" FASTA_HOST="$(/usr/bin/uname -n)" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fasta3/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fasta3/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fasta3/work/.cache HOME=/wrkdirs/usr/ports/biology/fasta3/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fasta3/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fasta3/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- VER="36" PORTDOCS="" PORTEXAMPLES="" OSREL=13.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/fasta3" EXAMPLESDIR="share/examples/fasta3" DATADIR="share/fasta3" WWWDIR="www/fasta3" ETCDIR="etc/fasta3" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fasta3 DOCSDIR=/usr/local/share/doc/fasta3 EXAMPLESDIR=/usr/local/share/examples/fasta3 WWWDIR=/usr/local/www/fasta3 ETCDIR=/usr/local/etc/fasta3 --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 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fasta3-36.3.8_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> fasta3-36.3.8_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of fasta3-36.3.8_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by fasta3-36.3.8_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by fasta3-36.3.8_1 for building => SHA256 Checksum OK for fasta3/2014-01-29/fasta-36.3.8.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by fasta3-36.3.8_1 for building ===> Extracting for fasta3-36.3.8_1 => SHA256 Checksum OK for fasta3/2014-01-29/fasta-36.3.8.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 fasta3-36.3.8_1 ===> Applying FreeBSD patches for fasta3-36.3.8_1 from /usr/ports/biology/fasta3/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fasta3-36.3.8_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. ===> fasta3-36.3.8_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of fasta3-36.3.8_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for fasta3-36.3.8_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for fasta3-36.3.8_1 --- init_sw.o --- --- lwm_align.o --- --- calcons_sw.o --- --- comp_mlib9.o --- --- compacc2_s.o --- --- lshowalign.o --- --- init_lal.o --- --- droplal2.o --- --- calcons_la.o --- --- init_fs.o --- --- init_fx.o --- --- init_tfx.o --- --- drop_tfx.o --- --- init_fy.o --- --- init_tfy.o --- --- drop_tfz.o --- --- init_tfs.o --- --- drop_tfs.o --- --- calcons_tfs.o --- --- init_fm.o --- --- tatstats_fm.o --- --- drop_fm.o --- --- calcons_fm.o --- --- mshowalign2_s.o --- --- init_tfm.o --- --- drop_tfm.o --- --- calcons_tfm.o --- --- init_ff.o --- --- scaleswtf.o --- --- tatstats_ff.o --- --- calcons_ff.o --- --- init_tf.o --- --- drop_tff.o --- --- calcons_tff.o --- --- scale_sn.o --- --- init_lnw.o --- --- gwm_align.o --- --- init_gnw.o --- --- dropgnw.o --- --- comp_mthr9.o --- --- work_thr2.o --- --- pthr_subs2.o --- --- compacc2_t.o --- --- showbest.o --- --- build_ares.o --- --- re_getlib.o --- --- mshowalign2_t.o --- --- htime.o --- --- apam.o --- --- doinit.o --- --- init_fa.o --- --- scale_se.o --- --- karlin.o --- --- drop_nfa.o --- --- wm_align.o --- --- calcons_fa.o --- --- lgetlib.o --- --- lgetaa_m.o --- --- c_dispn.o --- --- ncbl2_mlib.o --- --- lib_sel.o --- --- url_subs.o --- --- mrandom.o --- --- dropgsw2.o --- --- init_sw.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DSSEARCH initfa.c -o init_sw.o --- lwm_align.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c wm_align.c -o lwm_align.o --- calcons_sw.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DSSEARCH -c cal_cons2.c -o calcons_sw.o --- comp_mlib9.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DCOMP_MLIB -c comp_lib9.c -o comp_mlib9.o --- compacc2_s.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DCOMP_MLIB -c compacc2e.c -o compacc2_s.o --- lshowalign.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DLALIGN -c mshowalign2.c -o lshowalign.o --- init_lal.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DLALIGN initfa.c -o init_lal.o --- droplal2.o --- cc -DLALIGN -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropgsw2.c -o droplal2.o --- calcons_la.o --- cc -DLALIGN -DLCAL_CONS -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c cal_cons2.c -o calcons_la.o --- init_fs.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTS initfa.c -o init_fs.o --- init_fx.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTX initfa.c -o init_fx.o --- init_tfx.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTX -DTFAST initfa.c -o init_tfx.o --- drop_tfx.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DTFAST dropfx2.c -o drop_tfx.o --- init_fy.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTY initfa.c -o init_fy.o --- init_tfy.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTY -DTFAST initfa.c -o init_tfy.o --- drop_tfz.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DTFAST dropfz3.c -o drop_tfz.o --- init_tfs.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTS -DTFAST initfa.c -o init_tfs.o --- drop_tfs.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DTFAST -DFASTS dropfs2.c -o drop_tfs.o --- calcons_tfs.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DTFAST -DFASTS -c cal_consf.c -o calcons_tfs.o --- init_fm.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTM initfa.c -o init_fm.o --- tatstats_fm.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTM tatstats.c -o tatstats_fm.o --- drop_fm.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTM dropfs2.c -o drop_fm.o --- calcons_fm.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTM -c cal_consf.c -o calcons_fm.o --- mshowalign2_s.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c mshowalign2.c -o mshowalign2_s.o --- init_tfm.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTM -DTFAST initfa.c -o init_tfm.o --- drop_tfm.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DTFAST -DFASTM dropfs2.c -o drop_tfm.o --- calcons_tfm.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DTFAST -DFASTM -c cal_consf.c -o calcons_tfm.o --- init_ff.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTF initfa.c -o init_ff.o --- scaleswtf.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTF -c scaleswt.c -o scaleswtf.o --- tatstats_ff.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTF tatstats.c -o tatstats_ff.o --- calcons_ff.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTF -c cal_consf.c -o calcons_ff.o --- init_tf.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTF -DTFAST initfa.c -o init_tf.o --- drop_tff.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTF -DTFAST dropff2.c -o drop_tff.o --- calcons_tff.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DTFAST -DFASTF -c cal_consf.c -o calcons_tff.o --- scale_sn.o --- cc -DNORMAL_DIST -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c scaleswn.c -o scale_sn.o --- init_lnw.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DGLSEARCH initfa.c -o init_lnw.o --- gwm_align.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DGGSEARCH -c wm_align.c -o gwm_align.o --- init_gnw.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DGGSEARCH initfa.c -o init_gnw.o --- dropgnw.o --- cc -DGLOBAL_GLOBAL -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropnnw2.c -o dropgnw.o --- comp_mthr9.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DCOMP_THR -DCOMP_MLIB -c comp_lib9.c -o comp_mthr9.o --- work_thr2.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c work_thr2.c --- pthr_subs2.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c pthr_subs2.c --- compacc2_t.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DCOMP_THR -DCOMP_MLIB -c compacc2e.c -o compacc2_t.o --- showbest.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c mshowbest.c -o showbest.o --- build_ares.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c build_ares.c -o build_ares.o --- re_getlib.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c re_getlib.c --- mshowalign2_t.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DCOMP_THR -c mshowalign2.c -o mshowalign2_t.o --- htime.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c htime.c --- apam.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c apam.c --- doinit.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c doinit.c --- init_fa.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTA initfa.c -o init_fa.o --- scale_se.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DLOCAL_SCORE -c scaleswn.c -o scale_se.o --- karlin.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c karlin.c --- drop_nfa.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropnfa.c -o drop_nfa.o --- wm_align.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c wm_align.c -o wm_align.o --- calcons_fa.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTA -c cal_cons2.c -o calcons_fa.o --- lgetlib.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c nmgetlib.c -o lgetlib.o --- lgetaa_m.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c mmgetaa.c -o lgetaa_m.o --- ncbl2_mlib.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c ncbl2_mlib.c -o ncbl2_mlib.o --- lib_sel.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c lib_sel.c --- mrandom.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c mrandom.c -o mrandom.o --- dropgsw2.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropgsw2.c -o dropgsw2.o --- pssm_asn_subs.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c pssm_asn_subs.c --- url_subs.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c url_subs.c --- last_thresh.o --- --- lsim4.o --- --- c_dispn.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c c_dispn.c --- last_thresh.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c last_thresh.c --- lsim4.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c lsim4.c --- scaleswts.o --- --- last_tat.o --- --- tatstats_fs.o --- --- drop_fs2.o --- --- calcons_fs.o --- --- faatran.o --- --- tatstats_fs.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTS tatstats.c -o tatstats_fs.o --- last_tat.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c last_tat.c --- url_subs.o --- url_subs.c:154:43: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] 154 | if (pgm[0]=='t' || !strcmp(pgm,"fx") || !strcmp(pgm,"fy")==0 ) { | ^ ~~ url_subs.c:154:43: note: add parentheses after the '!' to evaluate the comparison first 154 | if (pgm[0]=='t' || !strcmp(pgm,"fx") || !strcmp(pgm,"fy")==0 ) { | ^ | ( ) url_subs.c:154:43: note: add parentheses around left hand side expression to silence this warning 154 | if (pgm[0]=='t' || !strcmp(pgm,"fx") || !strcmp(pgm,"fy")==0 ) { | ^ | ( ) 1 warning generated. --- calcons_fa.o --- cal_cons2.c:894:18: warning: parameter 'show_code' was not declared, defaults to 'int'; ISO C99 and later do not support implicit int [-Wimplicit-int] 894 | init_update_data(show_code) { | ^ cal_cons2.c:894:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 894 | init_update_data(show_code) { | ^ 2 warnings generated. --- showbest.o --- mshowbest.c:404:11: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses] 404 | if (!bbp->have_ares & 0x1) { | ^ ~ mshowbest.c:404:11: note: add parentheses after the '!' to evaluate the bitwise operator first 404 | if (!bbp->have_ares & 0x1) { | ^ | ( ) mshowbest.c:404:11: note: add parentheses around left hand side expression to silence this warning 404 | if (!bbp->have_ares & 0x1) { | ^ | ( ) 1 warning generated. --- drop_tff.o --- dropff2.c:684:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 684 | savemax (dptr, f_str) | ^ dropff2.c:1103:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1103 | kpsort (v, n) | ^ dropff2.c:1125:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1125 | krsort (v, n) | ^ 3 warnings generated. --- drop_fm.o --- dropfs2.c:1277:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1277 | kssort (v, n) | ^ dropfs2.c:1297:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1297 | kpsort (v, n) | ^ dropfs2.c:1329:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1329 | krsort (v, n) | ^ 3 warnings generated. --- calcons_la.o --- cal_cons2.c:894:18: warning: parameter 'show_code' was not declared, defaults to 'int'; ISO C99 and later do not support implicit int [-Wimplicit-int] 894 | init_update_data(show_code) { | ^ cal_cons2.c:894:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 894 | init_update_data(show_code) { | ^ 2 warnings generated. --- calcons_sw.o --- cal_cons2.c:894:18: warning: parameter 'show_code' was not declared, defaults to 'int'; ISO C99 and later do not support implicit int [-Wimplicit-int] 894 | init_update_data(show_code) { | ^ cal_cons2.c:894:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 894 | init_update_data(show_code) { | ^ 2 warnings generated. --- calcons_fs.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTS -c cal_consf.c -o calcons_fs.o --- scaleswts.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c scaleswt.c -o scaleswts.o --- drop_fs2.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTS -c dropfs2.c -o drop_fs2.o --- drop_fx.o --- --- drop_fz.o --- --- drop_ff2.o --- --- droplnw.o --- --- map_db --- --- init_tfm.o --- initfa.c:2046:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2046 | void sortbest (bptr, nbest, irelv) | ^ 1 warning generated. --- init_fm.o --- initfa.c:2046:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2046 | void sortbest (bptr, nbest, irelv) | ^ 1 warning generated. --- drop_tfs.o --- dropfs2.c:1277:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1277 | kssort (v, n) | ^ dropfs2.c:1297:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1297 | kpsort (v, n) | ^ dropfs2.c:1329:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1329 | krsort (v, n) | ^ 3 warnings generated. --- init_tfy.o --- initfa.c:2024:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2024 | void sortbest (bptr, nbest, irelv) | ^ 1 warning generated. --- init_tfx.o --- initfa.c:2024:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2024 | void sortbest (bptr, nbest, irelv) | ^ 1 warning generated. --- init_fx.o --- initfa.c:2024:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2024 | void sortbest (bptr, nbest, irelv) | ^ 1 warning generated. --- init_fs.o --- initfa.c:2046:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2046 | void sortbest (bptr, nbest, irelv) | ^ 1 warning generated. --- faatran.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c faatran.c --- drop_fx.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropfx2.c -o drop_fx.o --- drop_ff2.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTF dropff2.c -o drop_ff2.o --- map_db --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -o ../bin/map_db map_db.c --- init_tfs.o --- initfa.c:2046:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2046 | void sortbest (bptr, nbest, irelv) | ^ 1 warning generated. --- init_fy.o --- initfa.c:2024:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2024 | void sortbest (bptr, nbest, irelv) | ^ 1 warning generated. --- drop_tfm.o --- dropfs2.c:1277:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1277 | kssort (v, n) | ^ dropfs2.c:1297:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1297 | kpsort (v, n) | ^ dropfs2.c:1329:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1329 | krsort (v, n) | ^ 3 warnings generated. --- lgetlib.o --- nmgetlib.c:466:50: warning: passing arguments to 'ncbl2_closelib' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 466 | if (m_fptr->lb_type == NCBIBL20) ncbl2_closelib(m_fptr); | ^ 1 warning generated. --- init_fa.o --- initfa.c:2024:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2024 | void sortbest (bptr, nbest, irelv) | ^ 1 warning generated. --- init_gnw.o --- initfa.c:2024:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2024 | void sortbest (bptr, nbest, irelv) | ^ 1 warning generated. --- map_db --- map_db.c:224:23: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 224 | while ((n1=get_entry(sbuff, sbuff_max, &d_pos, &s_pos)) > 0) { | ^ --- drop_fz.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropfz3.c -o drop_fz.o --- init_tf.o --- initfa.c:2046:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2046 | void sortbest (bptr, nbest, irelv) | ^ 1 warning generated. --- pssm_asn_subs.o --- pssm_asn_subs.c:31:5: 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] 31 | int parse_pssm2_asn(); | ^ pssm_asn_subs.c:1357:1: note: conflicting prototype is here 1357 | parse_pssm2_asn(struct asn_bstruct *asnp, | ^ pssm_asn_subs.c:30:5: 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] 30 | int parse_pssm_asn(); | ^ pssm_asn_subs.c:1446:1: note: conflicting prototype is here 1446 | parse_pssm_asn(FILE *afd, | ^ 2 warnings generated. --- drop_nfa.o --- dropnfa.c:1086:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1086 | kssort (v, n) | ^ 1 warning generated. --- droplnw.o --- cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropnnw2.c -o droplnw.o --- init_sw.o --- initfa.c:2024:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2024 | void sortbest (bptr, nbest, irelv) | ^ 1 warning generated. --- init_ff.o --- initfa.c:2046:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2046 | void sortbest (bptr, nbest, irelv) | ^ 1 warning generated. --- init_lal.o --- initfa.c:2024:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2024 | void sortbest (bptr, nbest, irelv) | ^ 1 warning generated. --- lgetaa_m.o --- mmgetaa.c:166:87: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] 166 | fprintf(stderr,"\n *** Warning *** database too large (%lld) for 32-bit mmap()\n",f_size); | ~~~~ ^~~~~~ | %ld mmgetaa.c:205:14: warning: format specifies type 'long long' but the argument has type 'off_t' (aka 'long') [-Wformat] 204 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", | ~~~~ | %ld 205 | bname,statbuf.st_size,f_size); | ^~~~~~~~~~~~~~~ mmgetaa.c:205:30: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] 204 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", | ~~~~ | %ld 205 | bname,statbuf.st_size,f_size); | ^~~~~~ mmgetaa.c:296:14: warning: format specifies type 'long long' but the argument has type 'off_t' (aka 'long') [-Wformat] 295 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", | ~~~~ | %ld 296 | sname,statbuf.st_size,f_size); | ^~~~~~~~~~~~~~~ mmgetaa.c:296:30: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] 295 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", | ~~~~ | %ld 296 | sname,statbuf.st_size,f_size); | ^~~~~~ mmgetaa.c:83:5: 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] 83 | int agetlibm(); void aranlibm(); | ^ mmgetaa.c:488:1: note: conflicting prototype is here 488 | agetlibm(unsigned char *seq, | ^ mmgetaa.c:83:22: 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] 83 | int agetlibm(); void aranlibm(); | ^ mmgetaa.c:617:1: note: conflicting prototype is here 617 | aranlibm(char *str, | ^ mmgetaa.c:85:6: 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] 85 | void vranlibm(); | ^ mmgetaa.c:725:1: note: conflicting prototype is here 725 | vranlibm(char *str, | ^ mmgetaa.c:86:5: 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] 86 | int gcg_getlibm(); | ^ mmgetaa.c:774:1: note: conflicting prototype is here 774 | gcg_getlibm(unsigned char *seq, | ^ mmgetaa.c:84:5: 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] 84 | int lgetlibm(); void lranlibm(); | ^ mmgetaa.c:912:1: note: conflicting prototype is here 912 | lgetlibm(unsigned char *seq, | ^ mmgetaa.c:84:22: 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] 84 | int lgetlibm(); void lranlibm(); | ^ mmgetaa.c:1048:1: note: conflicting prototype is here 1048 | lranlibm(char *str, | ^ mmgetaa.c:1076:10: warning: format specifies type 'long long' but the argument has type 'MM_OFF' (aka 'long') [-Wformat] 1075 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", | ~~~~ | %ld 1076 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], | ^~~~~~~~~~~~~~~~~~ mmgetaa.c:1076:29: warning: format specifies type 'long long' but the argument has type 'MM_OFF' (aka 'long') [-Wformat] 1075 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", | ~~~~ | %ld 1076 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], | ^~~~~~~~~~~~~~~~~~ mmgetaa.c:1077:8: warning: format specifies type 'long long' but the argument has type 'MM_OFF' (aka 'long') [-Wformat] 1075 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", | ~~~~ | %ld 1076 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], 1077 | m_fd->d_pos_arr[i+1]-m_fd->s_pos_arr[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 14 warnings generated. --- drop_fs2.o --- dropfs2.c:1277:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1277 | kssort (v, n) | ^ dropfs2.c:1297:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1297 | kpsort (v, n) | ^ dropfs2.c:1329:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1329 | krsort (v, n) | ^ 3 warnings generated. --- compacc2_s.o --- compacc2e.c:2502:28: warning: format specifies type 'long long' but the argument has type 'off_t' (aka 'long') [-Wformat] 2494 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", | ~~~~~ | %8ld 2495 | rbuf_dp->mseq->libstr, rbuf_dp->seq->n1,rbuf_dp->frame,rbuf_rp->rst.comp,rbuf_rp->rst.H, 2496 | rbuf_rp->rst.score[0],rbuf_rp->rst.score[1],rbuf_rp->rst.score[2], 2497 | t_valid_stat, rbuf_rp->rst.alg_info, 2498 | (rbuf_rp->r_rst.score[0]<0 ? -1 : rbuf_rp->r_rst.score[0]), 2499 | (rbuf_rp->r_rst.score[1]<0 ? -1 : rbuf_rp->r_rst.score[1]), 2500 | (rbuf_rp->r_rst.score[2]<0 ? -1 : rbuf_rp->r_rst.score[2]), 2501 | tr_valid_stat, rbuf_rp->r_rst.alg_info, 2502 | rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); | ^~~~~~~~~~~~~~~~~~~~ compacc2e.c:2686:28: warning: format specifies type 'long long' but the argument has type 'off_t' (aka 'long') [-Wformat] 2678 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", | ~~~~~ | %8ld 2679 | rbuf_dp->mseq->libstr, rbuf_dp->seq->n1,rbuf_dp->frame,rbuf_rp->rst.comp,rbuf_rp->rst.H, 2680 | rbuf_rp->rst.score[0],rbuf_rp->rst.score[1],rbuf_rp->rst.score[2], 2681 | rbuf_rp->is_valid_stat, rbuf_rp->rst.alg_info, 2682 | (rbuf_rp->r_rst.score[0]<0 ? -1 : rbuf_rp->r_rst.score[0]), 2683 | (rbuf_rp->r_rst.score[1]<0 ? -1 : rbuf_rp->r_rst.score[1]), 2684 | (rbuf_rp->r_rst.score[2]<0 ? -1 : rbuf_rp->r_rst.score[2]), 2685 | rbuf_rp->is_valid_stat, rbuf_rp->r_rst.alg_info, 2686 | rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); | ^~~~~~~~~~~~~~~~~~~~ 2 warnings generated. --- map_db --- 1 warning generated. --- init_lnw.o --- initfa.c:2024:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2024 | void sortbest (bptr, nbest, irelv) | ^ 1 warning generated. --- ncbl2_mlib.o --- ncbl2_mlib.c:1087:8: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] 1086 | fprintf(stderr," could not read sequence record: %lld %ld != %ld\n", | ~~~~ | %ld 1087 | *libpos,tmp,seq_len); | ^~~~~~~ ncbl2_mlib.c:1131:60: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] 1131 | error: fprintf(stderr," error reading %s at %lld\n",libstr,*libpos); | ~~~~ ^~~~~~~ | %ld ncbl2_mlib.c:1416:10: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] 1415 | " could not read sequence record: %s %lld %ld != %ld: %d\n", | ~~~~ | %ld 1416 | libstr,*libpos,tmp,seqcnt,*seq); | ^~~~~~~ ncbl2_mlib.c:1436:3: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] 1435 | fprintf(stderr," could not read sequence record: %lld %ld/%ld\n", | ~~~~ | %ld 1436 | *libpos,tmp,seqcnt); | ^~~~~~~ ncbl2_mlib.c:1659:60: warning: format specifies type 'long long' but the argument has type 'fseek_t' (aka 'long') [-Wformat] 1659 | error: fprintf(stderr," error reading %s at %lld\n",libstr,*libpos); | ~~~~ ^~~~~~~ | %ld 5 warnings generated. --- drop_tfz.o --- dropfz3.c:1312:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1312 | kssort (v, n) | ^ dropfz3.c:1424:41: warning: passing arguments to 'ckalloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1424 | f_str->cur = (struct sx_s *) ckalloc(sizeof(struct sx_s)*sp); | ^ dropfz3.c:1428:41: warning: passing arguments to 'ckalloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1428 | f_str->cur = (struct sx_s *) ckalloc(sizeof(struct sx_s)*sp); | ^ dropfz3.c:1409:9: 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] 1409 | void *ckalloc(); | ^ dropfz3.c:1548:7: note: conflicting prototype is here 1548 | void *ckalloc(size_t amount) | ^ dropfz3.c:1580:7: 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 previous declaration [-Wdeprecated-non-prototype] 1580 | void *ckalloc(); | ^ dropfz3.c:1548:7: note: conflicting prototype is here 1548 | void *ckalloc(size_t amount) | ^ dropfz3.c:1609:21: warning: passing arguments to 'local_align' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1609 | score= local_align(&x, &y, &ex, &ey, | ^ dropfz3.c:1622:17: warning: passing arguments to 'global' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1622 | align = global(x, y, ex, ey, | ^ dropfz3.c:1582:12: 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] 1582 | static int local_align(), find_best(); | ^ dropfz3.c:1656:1: note: conflicting prototype is here 1656 | local_align(int *x, int *y, int *ex, int *ey, | ^ dropfz3.c:1682:12: warning: passing arguments to 'init_row2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1682 | init_row2(st_up, ld+5); | ^ dropfz3.c:1686:11: warning: passing arguments to 'init_ROW' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1686 | init_ROW(f_str->up, ld+1); | ^ dropfz3.c:1687:11: warning: passing arguments to 'init_ROW' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1687 | init_ROW(f_str->down, ld+1); | ^ dropfz3.c:1583:13: 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] 1583 | static void init_row2(), init_ROW(); | ^ dropfz3.c:1903:1: note: conflicting prototype is here 1903 | init_row2(int *row, int ld) { | ^ dropfz3.c:1583:26: 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] 1583 | static void init_row2(), init_ROW(); | ^ dropfz3.c:1908:13: note: conflicting prototype is here 1908 | static void init_ROW(st_ptr row, int ld) { | ^ dropfz3.c:1581:34: 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] 1581 | static match_ptr small_global(), global(); | ^ dropfz3.c:1937:1: note: conflicting prototype is here 1937 | global(int x, int y, int ex, int ey, | ^ dropfz3.c:1978:24: warning: passing arguments to 'small_global' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1978 | return small_global(x,y,ex,ey,wgts, gop, gext, dnap, pro, N1, N2,f_str); | ^ dropfz3.c:2004:16: warning: passing arguments to 'find_best' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2004 | if (find_best(f_str->up, f_str->down, &m1, &m2, ey-y+1, y, gop)) { | ^ dropfz3.c:1582:27: 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] 1582 | static int local_align(), find_best(); | ^ dropfz3.c:2023:1: note: conflicting prototype is here 2023 | find_best(st_ptr up, st_ptr down, int *m1, int *m2, int ld, int y, int gop) { | ^ dropfz3.c:1581:18: 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] 1581 | static match_ptr small_global(), global(); | ^ dropfz3.c:2052:1: note: conflicting prototype is here 2052 | small_global(int x, int y, int ex, int ey, | ^ dropfz3.c:2257:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2257 | fatal(msg) | ^ dropfz3.c:3587:18: warning: parameter 'show_code' was not declared, defaults to 'int'; ISO C99 and later do not support implicit int [-Wimplicit-int] 3587 | init_update_data(show_code) { | ^ dropfz3.c:3587:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3587 | init_update_data(show_code) { | ^ 21 warnings generated. --- lalign36 --- cc -o ../bin/lalign36 comp_mlib9.o compacc2_s.o showbest.o build_ares.o re_getlib.o lshowalign.o htime.o apam.o doinit.o init_lal.o droplal2.o lsim4.o calcons_la.o scale_se.o karlin.o last_thresh.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz --- compacc2_t.o --- compacc2e.c:2502:28: warning: format specifies type 'long long' but the argument has type 'off_t' (aka 'long') [-Wformat] 2494 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", | ~~~~~ | %8ld 2495 | rbuf_dp->mseq->libstr, rbuf_dp->seq->n1,rbuf_dp->frame,rbuf_rp->rst.comp,rbuf_rp->rst.H, 2496 | rbuf_rp->rst.score[0],rbuf_rp->rst.score[1],rbuf_rp->rst.score[2], 2497 | t_valid_stat, rbuf_rp->rst.alg_info, 2498 | (rbuf_rp->r_rst.score[0]<0 ? -1 : rbuf_rp->r_rst.score[0]), 2499 | (rbuf_rp->r_rst.score[1]<0 ? -1 : rbuf_rp->r_rst.score[1]), 2500 | (rbuf_rp->r_rst.score[2]<0 ? -1 : rbuf_rp->r_rst.score[2]), 2501 | tr_valid_stat, rbuf_rp->r_rst.alg_info, 2502 | rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); | ^~~~~~~~~~~~~~~~~~~~ compacc2e.c:2686:28: warning: format specifies type 'long long' but the argument has type 'off_t' (aka 'long') [-Wformat] 2678 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", | ~~~~~ | %8ld 2679 | rbuf_dp->mseq->libstr, rbuf_dp->seq->n1,rbuf_dp->frame,rbuf_rp->rst.comp,rbuf_rp->rst.H, 2680 | rbuf_rp->rst.score[0],rbuf_rp->rst.score[1],rbuf_rp->rst.score[2], 2681 | rbuf_rp->is_valid_stat, rbuf_rp->rst.alg_info, 2682 | (rbuf_rp->r_rst.score[0]<0 ? -1 : rbuf_rp->r_rst.score[0]), 2683 | (rbuf_rp->r_rst.score[1]<0 ? -1 : rbuf_rp->r_rst.score[1]), 2684 | (rbuf_rp->r_rst.score[2]<0 ? -1 : rbuf_rp->r_rst.score[2]), 2685 | rbuf_rp->is_valid_stat, rbuf_rp->r_rst.alg_info, 2686 | rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); | ^~~~~~~~~~~~~~~~~~~~ 2 warnings generated. --- ssearch36 --- --- glsearch36 --- --- ggsearch36 --- --- fasta36 --- --- fasts36 --- --- fastm36 --- --- tfastf36 --- --- tfasts36 --- --- tfastm36 --- --- tfasty36 --- --- ssearch36 --- cc -o ../bin/ssearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_sw.o dropgsw2.o lwm_align.o calcons_sw.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread --- glsearch36 --- cc -o ../bin/glsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_lnw.o droplnw.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread --- ggsearch36 --- cc -o ../bin/ggsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_gnw.o dropgnw.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread --- fasta36 --- cc -o ../bin/fasta36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fa.o drop_nfa.o wm_align.o calcons_fa.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread --- fasts36 --- cc -o ../bin/fasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fs.o drop_fs2.o calcons_fs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread --- fastm36 --- cc -o ../bin/fastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fm.o drop_fm.o calcons_fm.o scaleswts.o last_tat.o tatstats_fm.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread --- tfasts36 --- cc -o ../bin/tfasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfs.o drop_tfs.o calcons_tfs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread --- tfastf36 --- cc -o ../bin/tfastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tf.o drop_tff.o calcons_tff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread --- tfastm36 --- cc -o ../bin/tfastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_s.o htime.o apam.o doinit.o init_tfm.o drop_tfm.o calcons_tfm.o scaleswts.o tatstats_fm.o last_tat.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread --- tfasty36 --- cc -o ../bin/tfasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfy.o drop_tfz.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lz -pthread --- drop_tfx.o --- dropfx2.c:1208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1208 | kssort (v, n) | ^ dropfx2.c:1283:41: warning: passing arguments to 'ckalloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1283 | f_str->cur = (struct sx_s *) ckalloc(sizeof(struct sx_s)*sp); | ^ dropfx2.c:1288:41: warning: passing arguments to 'ckalloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1288 | f_str->cur = (struct sx_s *) ckalloc(sizeof(struct sx_s)*sp); | ^ dropfx2.c:1272:9: 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] 1272 | void *ckalloc(); | ^ dropfx2.c:1416:7: note: conflicting prototype is here 1416 | void *ckalloc(size_t amount) | ^ dropfx2.c:1493:21: warning: passing arguments to 'local_align' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1493 | score= local_align(&x, &y, &ex, &ey, pam_matrix, | ^ dropfx2.c:1508:17: warning: passing arguments to 'global' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1508 | align = global(x, y, ex, ey, pam_matrix, gopen, gex, gshift, | ^ dropfx2.c:1460:12: 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] 1460 | static int local_align(), find_best(); | ^ dropfx2.c:1550:1: note: conflicting prototype is here 1550 | local_align(int *x, int *y, int *ex, int *ey, | ^ dropfx2.c:1576:12: warning: passing arguments to 'init_row2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1576 | init_row2(st_up, ld+5); | ^ dropfx2.c:1579:11: warning: passing arguments to 'init_ROW' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1579 | init_ROW(up, ld+1); /* set to zero */ | ^ dropfx2.c:1580:11: warning: passing arguments to 'init_ROW' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1580 | init_ROW(down, ld+1); /* set to zero */ | ^ dropfx2.c:1461:13: 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] 1461 | static void init_row2(), init_ROW(); | ^ dropfx2.c:1807:1: note: conflicting prototype is here 1807 | init_row2(int *row, int ld) { | ^ dropfx2.c:1461:27: 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] 1461 | static void init_row2(), init_ROW(); | ^ dropfx2.c:1813:1: note: conflicting prototype is here 1813 | init_ROW(st_ptr row, int ld) { | ^ dropfx2.c:1459:34: 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] 1459 | static match_ptr small_global(), global(); | ^ dropfx2.c:1842:1: note: conflicting prototype is here 1842 | global(int x, int y, int ex, int ey, | ^ dropfx2.c:1888:24: warning: passing arguments to 'small_global' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1888 | return small_global(x,y,ex,ey, | ^ dropfx2.c:1917:16: warning: passing arguments to 'find_best' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1917 | if (find_best(*up_stp, *dn_stp, &m1, &m2, ey-y+1, y, gop)) { | ^ dropfx2.c:1460:27: 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] 1460 | static int local_align(), find_best(); | ^ dropfx2.c:1940:1: note: conflicting prototype is here 1940 | find_best(st_ptr up, st_ptr down, | ^ dropfx2.c:1459:18: 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] 1459 | static match_ptr small_global(), global(); | ^ dropfx2.c:1970:1: note: conflicting prototype is here 1970 | small_global(int x, int y, int ex, int ey, | ^ dropfx2.c:2155:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2155 | void fatal(msg) | ^ dropfx2.c:3613:18: warning: parameter 'show_code' was not declared, defaults to 'int'; ISO C99 and later do not support implicit int [-Wimplicit-int] 3613 | init_update_data(show_code) { | ^ dropfx2.c:3613:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3613 | init_update_data(show_code) { | ^ 20 warnings generated. --- tfastx36 --- --- drop_fx.o --- dropfx2.c:1208:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1208 | kssort (v, n) | ^ dropfx2.c:1283:41: warning: passing arguments to 'ckalloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1283 | f_str->cur = (struct sx_s *) ckalloc(sizeof(struct sx_s)*sp); | ^ dropfx2.c:1288:41: warning: passing arguments to 'ckalloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1288 | f_str->cur = (struct sx_s *) ckalloc(sizeof(struct sx_s)*sp); | ^ dropfx2.c:1272:9: 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] 1272 | void *ckalloc(); | ^ dropfx2.c:1416:7: note: conflicting prototype is here 1416 | void *ckalloc(size_t amount) | ^ dropfx2.c:1493:21: warning: passing arguments to 'local_align' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1493 | score= local_align(&x, &y, &ex, &ey, pam_matrix, | ^ dropfx2.c:1508:17: warning: passing arguments to 'global' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1508 | align = global(x, y, ex, ey, pam_matrix, gopen, gex, gshift, | ^ dropfx2.c:1460:12: 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] 1460 | static int local_align(), find_best(); | ^ dropfx2.c:1550:1: note: conflicting prototype is here 1550 | local_align(int *x, int *y, int *ex, int *ey, | ^ dropfx2.c:1576:12: warning: passing arguments to 'init_row2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1576 | init_row2(st_up, ld+5); | ^ dropfx2.c:1579:11: warning: passing arguments to 'init_ROW' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1579 | init_ROW(up, ld+1); /* set to zero */ | ^ dropfx2.c:1580:11: warning: passing arguments to 'init_ROW' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1580 | init_ROW(down, ld+1); /* set to zero */ | ^ dropfx2.c:1461:13: 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] 1461 | static void init_row2(), init_ROW(); | ^ dropfx2.c:1807:1: note: conflicting prototype is here 1807 | init_row2(int *row, int ld) { | ^ dropfx2.c:1461:27: 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] 1461 | static void init_row2(), init_ROW(); | ^ dropfx2.c:1813:1: note: conflicting prototype is here 1813 | init_ROW(st_ptr row, int ld) { | ^ dropfx2.c:1459:34: 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] 1459 | static match_ptr small_global(), global(); | ^ dropfx2.c:1842:1: note: conflicting prototype is here 1842 | global(int x, int y, int ex, int ey, | ^ dropfx2.c:1888:24: warning: passing arguments to 'small_global' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1888 | return small_global(x,y,ex,ey, | ^ dropfx2.c:1917:16: warning: passing arguments to 'find_best' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1917 | if (find_best(*up_stp, *dn_stp, &m1, &m2, ey-y+1, y, gop)) { | ^ dropfx2.c:1460:27: 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] 1460 | static int local_align(), find_best(); | ^ dropfx2.c:1940:1: note: conflicting prototype is here 1940 | find_best(st_ptr up, st_ptr down, | ^ dropfx2.c:1459:18: 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] 1459 | static match_ptr small_global(), global(); | ^ dropfx2.c:1970:1: note: conflicting prototype is here 1970 | small_global(int x, int y, int ex, int ey, | ^ dropfx2.c:2155:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2155 | void fatal(msg) | ^ dropfx2.c:3613:18: warning: parameter 'show_code' was not declared, defaults to 'int'; ISO C99 and later do not support implicit int [-Wimplicit-int] 3613 | init_update_data(show_code) { | ^ dropfx2.c:3613:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3613 | init_update_data(show_code) { | ^ 20 warnings generated. --- fastx36 --- cc -o ../bin/fastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fx.o drop_fx.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread --- drop_ff2.o --- dropff2.c:684:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 684 | savemax (dptr, f_str) | ^ dropff2.c:1103:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1103 | kpsort (v, n) | ^ dropff2.c:1125:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1125 | krsort (v, n) | ^ 3 warnings generated. --- fastf36 --- cc -o ../bin/fastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_ff.o drop_ff2.o calcons_ff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread --- tfastx36 --- cc -o ../bin/tfastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfx.o drop_tfx.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lz -pthread --- drop_fz.o --- dropfz3.c:1312:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1312 | kssort (v, n) | ^ dropfz3.c:1424:41: warning: passing arguments to 'ckalloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1424 | f_str->cur = (struct sx_s *) ckalloc(sizeof(struct sx_s)*sp); | ^ dropfz3.c:1428:41: warning: passing arguments to 'ckalloc' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1428 | f_str->cur = (struct sx_s *) ckalloc(sizeof(struct sx_s)*sp); | ^ dropfz3.c:1409:9: 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] 1409 | void *ckalloc(); | ^ dropfz3.c:1548:7: note: conflicting prototype is here 1548 | void *ckalloc(size_t amount) | ^ dropfz3.c:1580:7: 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 previous declaration [-Wdeprecated-non-prototype] 1580 | void *ckalloc(); | ^ dropfz3.c:1548:7: note: conflicting prototype is here 1548 | void *ckalloc(size_t amount) | ^ dropfz3.c:1609:21: warning: passing arguments to 'local_align' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1609 | score= local_align(&x, &y, &ex, &ey, | ^ dropfz3.c:1622:17: warning: passing arguments to 'global' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1622 | align = global(x, y, ex, ey, | ^ dropfz3.c:1582:12: 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] 1582 | static int local_align(), find_best(); | ^ dropfz3.c:1656:1: note: conflicting prototype is here 1656 | local_align(int *x, int *y, int *ex, int *ey, | ^ dropfz3.c:1682:12: warning: passing arguments to 'init_row2' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1682 | init_row2(st_up, ld+5); | ^ dropfz3.c:1686:11: warning: passing arguments to 'init_ROW' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1686 | init_ROW(f_str->up, ld+1); | ^ dropfz3.c:1687:11: warning: passing arguments to 'init_ROW' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1687 | init_ROW(f_str->down, ld+1); | ^ dropfz3.c:1583:13: 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] 1583 | static void init_row2(), init_ROW(); | ^ dropfz3.c:1903:1: note: conflicting prototype is here 1903 | init_row2(int *row, int ld) { | ^ dropfz3.c:1583:26: 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] 1583 | static void init_row2(), init_ROW(); | ^ dropfz3.c:1908:13: note: conflicting prototype is here 1908 | static void init_ROW(st_ptr row, int ld) { | ^ dropfz3.c:1581:34: 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] 1581 | static match_ptr small_global(), global(); | ^ dropfz3.c:1937:1: note: conflicting prototype is here 1937 | global(int x, int y, int ex, int ey, | ^ dropfz3.c:1978:24: warning: passing arguments to 'small_global' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1978 | return small_global(x,y,ex,ey,wgts, gop, gext, dnap, pro, N1, N2,f_str); | ^ dropfz3.c:2004:16: warning: passing arguments to 'find_best' without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2004 | if (find_best(f_str->up, f_str->down, &m1, &m2, ey-y+1, y, gop)) { | ^ dropfz3.c:1582:27: 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] 1582 | static int local_align(), find_best(); | ^ dropfz3.c:2023:1: note: conflicting prototype is here 2023 | find_best(st_ptr up, st_ptr down, int *m1, int *m2, int ld, int y, int gop) { | ^ dropfz3.c:1581:18: 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] 1581 | static match_ptr small_global(), global(); | ^ dropfz3.c:2052:1: note: conflicting prototype is here 2052 | small_global(int x, int y, int ex, int ey, | ^ dropfz3.c:2257:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 2257 | fatal(msg) | ^ dropfz3.c:3587:18: warning: parameter 'show_code' was not declared, defaults to 'int'; ISO C99 and later do not support implicit int [-Wimplicit-int] 3587 | init_update_data(show_code) { | ^ dropfz3.c:3587:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 3587 | init_update_data(show_code) { | ^ 21 warnings generated. --- fasty36 --- cc -o ../bin/fasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fy.o drop_fz.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for fasta3-36.3.8_1 ===> Generating temporary packing list cc -o ../bin/fasta36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fa.o drop_nfa.o wm_align.o calcons_fa.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread cc -o ../bin/ssearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_sw.o dropgsw2.o lwm_align.o calcons_sw.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread cc -o ../bin/lalign36 comp_mlib9.o compacc2_s.o showbest.o build_ares.o re_getlib.o lshowalign.o htime.o apam.o doinit.o init_lal.o droplal2.o lsim4.o calcons_la.o scale_se.o karlin.o last_thresh.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz cc -o ../bin/fasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fs.o drop_fs2.o calcons_fs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread cc -o ../bin/fastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fx.o drop_fx.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread cc -o ../bin/tfastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfx.o drop_tfx.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lz -pthread cc -o ../bin/fasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fy.o drop_fz.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread cc -o ../bin/tfasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfy.o drop_tfz.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lz -pthread cc -o ../bin/tfasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfs.o drop_tfs.o calcons_tfs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread cc -o ../bin/fastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fm.o drop_fm.o calcons_fm.o scaleswts.o last_tat.o tatstats_fm.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread cc -o ../bin/tfastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_s.o htime.o apam.o doinit.o init_tfm.o drop_tfm.o calcons_tfm.o scaleswts.o tatstats_fm.o last_tat.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread cc -o ../bin/fastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_ff.o drop_ff2.o calcons_ff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread cc -o ../bin/tfastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tf.o drop_tff.o calcons_tff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread cc -o ../bin/glsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_lnw.o droplnw.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread cc -o ../bin/ggsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_gnw.o dropgnw.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkg.DaveG.ca' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -o ../bin/map_db map_db.c map_db.c:224:23: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 224 | while ((n1=get_entry(sbuff, sbuff_max, &d_pos, &s_pos)) > 0) { | ^ 1 warning generated. cd ../bin; cp fasta36 ssearch36 lalign36 fasts36 fastx36 tfastx36 fasty36 tfasty36 tfasts36 fastm36 tfastm36 fastf36 tfastf36 glsearch36 ggsearch36 map_db /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/bin; cd ../src (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/bin && install -s -m 555 * /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/bin) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/conf && install -m 0644 fastlibs /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/etc/fastlibs.sample) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 data/*.mat /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 444 fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 444 fastf3.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 444 fasts3.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 444 prss3.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 444 map_db.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 444 ps_lav.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/fastf35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/fasts35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/fastm35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/fastx35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/fasty35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/ggsearch35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/lalign35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/ssearch35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/tfasta35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/tfastf35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/tfasts35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/tfastx35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/tfasty35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/prfx35.1) (/bin/ln -sf fasta36.1 /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/man/man1/prss35.1) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 COPYRIGHT /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 FASTA_LIST /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 README /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 0644 README.versions /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 0644 fasta_func.doc /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 0644 readme.* /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 0644 fasta.defaults /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 0644 fasta.options /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 0644 fasta_versions.html /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8/doc && install -m 0644 changes*.html /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/doc/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 seq/*.aa /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/examples/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 seq/*.lc /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/examples/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 seq/*.seq /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/examples/fasta3) (cd /wrkdirs/usr/ports/biology/fasta3/work/fasta-36.3.8 && install -m 0644 seq/*.lib /wrkdirs/usr/ports/biology/fasta3/work/stage/usr/local/share/examples/fasta3) ====> 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=2025-12-11T04:59:48+0000' 'PKG_NOTE_ports_top_git_hash=62d8b1999233' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=1b819e486953' '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 fasta3-36.3.8_1 ===> Building fasta3-36.3.8_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for fasta3-36.3.8_1 build of biology/fasta3 | fasta3-36.3.8_1 ended at Thu Dec 11 00:00:05 EST 2025 build time: 00:00:18