Diff of the two buildlogs: -- --- b1/build.log 2025-09-24 13:49:31.623752356 +0000 +++ b2/build.log 2025-09-24 13:57:07.672295707 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Sep 24 01:44:46 -12 2025 -I: pbuilder-time-stamp: 1758721486 +I: Current time: Wed Oct 28 10:12:32 +14 2026 +I: pbuilder-time-stamp: 1793131952 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying gcc-15.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1317710/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3276862/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 27 20:13 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3276862/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3276862/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='048dec0d52a342c08f0937aa730fd187' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1317710' - PS1='# ' - PS2='> ' + INVOCATION_ID=4f318b415d934add940a55d44f5ede15 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3276862 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.dR8BUkoy/pbuilderrc_Hiwv --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dR8BUkoy/b1 --logfile b1/build.log fasta3_36.3.8i.14-Nov-2020-4.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.dR8BUkoy/pbuilderrc_gKSG --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dR8BUkoy/b2 --logfile b2/build.log fasta3_36.3.8i.14-Nov-2020-4.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1317710/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3276862/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -141,7 +173,7 @@ Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.27 [940 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-3 [467 kB] -Fetched 11.7 MB in 8s (1375 kB/s) +Fetched 11.7 MB in 7s (1704 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) @@ -276,7 +308,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/fasta3-36.3.8i.14-Nov-2020/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../fasta3_36.3.8i.14-Nov-2020-4_source.changes +I: user script /srv/workspace/pbuilder/3276862/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3276862/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/fasta3-36.3.8i.14-Nov-2020/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../fasta3_36.3.8i.14-Nov-2020-4_source.changes dpkg-buildpackage: info: source package fasta3 dpkg-buildpackage: info: source version 36.3.8i.14-Nov-2020-4 dpkg-buildpackage: info: source distribution unstable @@ -306,7 +342,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020' dh_auto_build --sourcedirectory make --builddirectory src --buildsystem makefile -- -f "../make/Makefile.linux64" - cd src && make -j40 INSTALL="install --strip-program=true" -f ../make/Makefile.linux64 + cd src && make -j42 INSTALL="install --strip-program=true" -f ../make/Makefile.linux64 make[2]: Entering directory '/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020/src' cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_THR -DCOMP_MLIB -c comp_lib9.c -o comp_mthr9.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c work_thr2.c @@ -347,21 +383,129 @@ cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c lsim4.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DLALIGN -DLCAL_CONS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c cal_cons2.c -o calcons_la.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS initfa.c -o init_fs.o +dropnfa.c: In function 'kssort': cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c scaleswt.c -o scaleswts.o +dropnfa.c:1092:1: warning: old-style function definition [-Wold-style-definition] + 1092 | kssort (v, n) + | ^~~~~~ cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c last_tat.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS tatstats.c -o tatstats_fs.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTS -c dropfs2.c -o drop_fs2.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTS -c cal_consf.c -o calcons_fs.o -dropnfa.c: In function 'kssort': -dropnfa.c:1092:1: warning: old-style function definition [-Wold-style-definition] - 1092 | kssort (v, n) - | ^~~~~~ cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTX initfa.c -o init_fx.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c faatran.c +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropfx2.c -o drop_fx.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTX -DTFAST initfa.c -o init_tfx.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST dropfx2.c -o drop_tfx.o +dropfs2.c: In function 'kssort': +dropfs2.c:1277:1: warning: old-style function definition [-Wold-style-definition] + 1277 | kssort (v, n) + | ^~~~~~ +dropfs2.c: In function 'kpsort': +dropfs2.c:1297:1: warning: old-style function definition [-Wold-style-definition] + 1297 | kpsort (v, n) + | ^~~~~~ +dropfs2.c: In function 'krsort': +dropfs2.c:1329:1: warning: old-style function definition [-Wold-style-definition] + 1329 | krsort (v, n) + | ^~~~~~ +mmgetaa.c: In function 'load_mmap': +mmgetaa.c:172:63: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'fseek_t' {aka 'long int'} [-Wformat=] + 172 | fprintf(stderr,"\n *** Warning *** database too large (%lld) for 32-bit mmap()\n",f_size); + | ~~~^ ~~~~~~ + | | | + | long long int fseek_t {aka long int} + | %ld +mmgetaa.c:210:41: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '__off_t' {aka 'long int'} [-Wformat=] + 210 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", + | ~~~^ + | | + | long long int + | %ld + 211 | bname,statbuf.st_size,f_size); + | ~~~~~~~~~~~~~~~ + | | + | __off_t {aka long int} +mmgetaa.c:210:66: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'fseek_t' {aka 'long int'} [-Wformat=] + 210 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", + | ~~~^ + | | + | long long int + | %ld + 211 | bname,statbuf.st_size,f_size); + | ~~~~~~ + | | + | fseek_t {aka long int} +mmgetaa.c:301:59: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '__off_t' {aka 'long int'} [-Wformat=] + 301 | fprintf(stderr,"*** ERROR [%s:%d] %s file size (%lld) and expected size (%lld) don't match\n", + | ~~~^ + | | + | long long int + | %ld + 302 | __FILE__, __LINE__, sname,statbuf.st_size,f_size); + | ~~~~~~~~~~~~~~~ + | | + | __off_t {aka long int} +mmgetaa.c:301:84: warning: format '%lld' expects argument of type 'long long int', but argument 7 has type 'fseek_t' {aka 'long int'} [-Wformat=] + 301 | fprintf(stderr,"*** ERROR [%s:%d] %s file size (%lld) and expected size (%lld) don't match\n", + | ~~~^ + | | + | long long int + | %ld + 302 | __FILE__, __LINE__, sname,statbuf.st_size,f_size); + | ~~~~~~ + | | + | fseek_t {aka long int} +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTY initfa.c -o init_fy.o +mmgetaa.c: In function 'check_mmap': +mmgetaa.c:1082:31: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'MM_OFF' {aka 'long int'} [-Wformat=] + 1082 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", + | ~~~^ + | | + | long long int + | %ld + 1083 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], + | ~~~~~~~~~~~~~~~~~~ + | | + | MM_OFF {aka long int} +mmgetaa.c:1082:37: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'MM_OFF' {aka 'long int'} [-Wformat=] + 1082 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", + | ~~~^ + | | + | long long int + | %ld + 1083 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], + | ~~~~~~~~~~~~~~~~~~ + | | + | MM_OFF {aka long int} +mmgetaa.c:1082:43: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'MM_OFF' {aka 'long int'} [-Wformat=] + 1082 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", + | ~~~^ + | | + | long long int + | %ld + 1083 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], + 1084 | m_fd->d_pos_arr[i+1]-m_fd->s_pos_arr[i]); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | + | MM_OFF {aka long int} +initfa.c: In function 'sortbest': +initfa.c:2048:6: warning: old-style function definition [-Wold-style-definition] + 2048 | void sortbest (bptr, nbest, irelv) + | ^~~~~~~~ +initfa.c: In function 'sortbest': +initfa.c:2070:6: warning: old-style function definition [-Wold-style-definition] + 2070 | void sortbest (bptr, nbest, irelv) + | ^~~~~~~~ initfa.c: In function 'sortbest': initfa.c:2048:6: warning: old-style function definition [-Wold-style-definition] 2048 | void sortbest (bptr, nbest, irelv) | ^~~~~~~~ +initfa.c: In function 'sortbest': +initfa.c:2048:6: warning: old-style function definition [-Wold-style-definition] + 2048 | void sortbest (bptr, nbest, irelv) + | ^~~~~~~~ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropfz3.c -o drop_fz.o nmgetlib.c: In function 'agetlib': nmgetlib.c:636:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 636 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR/2,lm_fd->libf); @@ -375,6 +519,7 @@ nmgetlib.c:696:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 696 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTY -DTFAST initfa.c -o init_tfy.o nmgetlib.c: In function 'aranlib': nmgetlib.c:716:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 716 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); @@ -389,6 +534,11 @@ nmgetlib.c:811:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 811 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR-strlen(lm_fd->lline),lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST dropfz3.c -o drop_tfz.o +initfa.c: In function 'sortbest': +initfa.c:2048:6: warning: old-style function definition [-Wold-style-definition] + 2048 | void sortbest (bptr, nbest, irelv) + | ^~~~~~~~ nmgetlib.c: In function 'qranlib': nmgetlib.c:834:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 834 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); @@ -397,9 +547,19 @@ nmgetlib.c:887:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 887 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'load_ncbl2': nmgetlib.c:925:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 925 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c:810:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 810 | fread(title_str,(size_t)1,(size_t)title_len,ifile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c:820:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 820 | fread(pdb_title_str,(size_t)1,(size_t)pdb_title_len,ifile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c:831:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 831 | fread(date_str,(size_t)1,(size_t)date_len,ifile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function 'lget_ann': nmgetlib.c:949:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fgets(desc,sizeof(desc),lm_fd->libf); @@ -423,16 +583,16 @@ nmgetlib.c:1041:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1041 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'ncbl2_ranlib': nmgetlib.c:1048:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1048 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mmgetaa.c: In function 'load_mmap': -mmgetaa.c:172:63: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'fseek_t' {aka 'long int'} [-Wformat=] - 172 | fprintf(stderr,"\n *** Warning *** database too large (%lld) for 32-bit mmap()\n",f_size); - | ~~~^ ~~~~~~ - | | | - | long long int fseek_t {aka long int} - | %ld +ncbl2_mlib.c:1720:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1720 | fread(str,(size_t)1,(size_t)(llen),m_fd->hfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c:1735:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1735 | fread(my_buff,(size_t)1,llen,m_fd->hfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function 'pgetlib': nmgetlib.c:1086:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1086 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); /* get the extra line */ @@ -440,46 +600,6 @@ nmgetlib.c:1108:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1108 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mmgetaa.c:210:41: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '__off_t' {aka 'long int'} [-Wformat=] - 210 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", - | ~~~^ - | | - | long long int - | %ld - 211 | bname,statbuf.st_size,f_size); - | ~~~~~~~~~~~~~~~ - | | - | __off_t {aka long int} -mmgetaa.c:210:66: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'fseek_t' {aka 'long int'} [-Wformat=] - 210 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", - | ~~~^ - | | - | long long int - | %ld - 211 | bname,statbuf.st_size,f_size); - | ~~~~~~ - | | - | fseek_t {aka long int} -mmgetaa.c:301:59: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '__off_t' {aka 'long int'} [-Wformat=] - 301 | fprintf(stderr,"*** ERROR [%s:%d] %s file size (%lld) and expected size (%lld) don't match\n", - | ~~~^ - | | - | long long int - | %ld - 302 | __FILE__, __LINE__, sname,statbuf.st_size,f_size); - | ~~~~~~~~~~~~~~~ - | | - | __off_t {aka long int} -mmgetaa.c:301:84: warning: format '%lld' expects argument of type 'long long int', but argument 7 has type 'fseek_t' {aka 'long int'} [-Wformat=] - 301 | fprintf(stderr,"*** ERROR [%s:%d] %s file size (%lld) and expected size (%lld) don't match\n", - | ~~~^ - | | - | long long int - | %ld - 302 | __FILE__, __LINE__, sname,statbuf.st_size,f_size); - | ~~~~~~ - | | - | fseek_t {aka long int} nmgetlib.c: In function 'pranlib': nmgetlib.c:1132:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1132 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); @@ -493,13 +613,38 @@ nmgetlib.c:1143:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1143 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'src_int4_read': +ncbl2_mlib.c:1841:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1841 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'src_long4_read': +ncbl2_mlib.c:1856:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1856 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'src_uint4_read': nmgetlib.c: In function 'egetlib': -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropfx2.c -o drop_fx.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTX -DTFAST initfa.c -o init_tfx.o -initfa.c: In function 'sortbest': +ncbl2_mlib.c:1869:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1869 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1227:1: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1227 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'src_long8_read': +ncbl2_mlib.c:1884:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1884 | fread((char *)&b[0],(size_t)1,(size_t)8,fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'ncbi_long8_read': +ncbl2_mlib.c:1904:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1904 | fread((char *)&b[0],(size_t)1,(size_t)8,fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'src_char_read': +ncbl2_mlib.c:1911:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1911 | fread(val,(size_t)1,(size_t)1,fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'src_fstr_read': +ncbl2_mlib.c:1916:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1916 | fread(val,(size_t)slen,(size_t)1,fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function 'eranlib': nmgetlib.c:1257:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1257 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); @@ -523,6 +668,9 @@ nmgetlib.c:1340:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1340 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS -DTFAST initfa.c -o init_tfs.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST -DFASTS dropfs2.c -o drop_tfs.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTS -c cal_consf.c -o calcons_tfs.o nmgetlib.c: In function 'iranlib': nmgetlib.c:1367:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1367 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); @@ -533,9 +681,6 @@ nmgetlib.c:1387:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1387 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -initfa.c:2048:6: warning: old-style function definition [-Wold-style-definition] - 2048 | void sortbest (bptr, nbest, irelv) - | ^~~~~~~~ nmgetlib.c: In function 'vgetlib': nmgetlib.c:1425:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1425 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); @@ -556,48 +701,25 @@ nmgetlib.c:1528:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1528 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mmgetaa.c: In function 'check_mmap': -ncbl2_mlib.c: In function 'load_ncbl2': -mmgetaa.c:1082:31: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'MM_OFF' {aka 'long int'} [-Wformat=] - 1082 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", - | ~~~^ - | | - | long long int - | %ld - 1083 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], - | ~~~~~~~~~~~~~~~~~~ - | | - | MM_OFF {aka long int} -mmgetaa.c:1082:37: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'MM_OFF' {aka 'long int'} [-Wformat=] - 1082 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", - | ~~~^ - | | - | long long int - | %ld - 1083 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], - | ~~~~~~~~~~~~~~~~~~ - | | - | MM_OFF {aka long int} -mmgetaa.c:1082:43: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'MM_OFF' {aka 'long int'} [-Wformat=] - 1082 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", - | ~~~^ - | | - | long long int - | %ld - 1083 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], - 1084 | m_fd->d_pos_arr[i+1]-m_fd->s_pos_arr[i]); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | MM_OFF {aka long int} -ncbl2_mlib.c:810:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 810 | fread(title_str,(size_t)1,(size_t)title_len,ifile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c:820:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 820 | fread(pdb_title_str,(size_t)1,(size_t)pdb_title_len,ifile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c:831:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 831 | fread(date_str,(size_t)1,(size_t)date_len,ifile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM initfa.c -o init_fm.o +dropfx2.c: In function 'pro_dna': +dropfx2.c:1528:18: warning: passing argument 9 of 'global' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] + 1528 | dna_prot_seq, prot_seq, 0, 0, &up, &down, &tp, + | ^~~~~~~~~~~~ +dropfx2.c:1476:112: note: expected 'unsigned char *' but argument is of type 'const unsigned char *' + 1476 | static match_ptr global(int x, int y, int ex, int ey, int **wgts, int gop, int gext, int shift, unsigned char *dnap, unsigned char *pro, int N1, int N2, st_ptr *up_stp, st_ptr *dn_stp, st_ptr *tp_stp, struct smgl_str *smgl_sp); + | ~~~~~~~~~~~~~~~^~~~ +dropfx2.c:1528:32: warning: passing argument 10 of 'global' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] + 1528 | dna_prot_seq, prot_seq, 0, 0, &up, &down, &tp, + | ^~~~~~~~ +dropfx2.c:1476:133: note: expected 'unsigned char *' but argument is of type 'const unsigned char *' + 1476 | static match_ptr global(int x, int y, int ex, int ey, int **wgts, int gop, int gext, int shift, unsigned char *dnap, unsigned char *pro, int N1, int N2, st_ptr *up_stp, st_ptr *dn_stp, st_ptr *tp_stp, struct smgl_str *smgl_sp); + | ~~~~~~~~~~~~~~~^~~ +initfa.c: In function 'sortbest': +initfa.c:2048:6: warning: old-style function definition [-Wold-style-definition] + 2048 | void sortbest (bptr, nbest, irelv) + | ^~~~~~~~ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM tatstats.c -o tatstats_fm.o nmgetlib.c: In function 'gcg_getlib': nmgetlib.c:1570:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1570 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); @@ -614,6 +736,10 @@ nmgetlib.c:1610:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1610 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +dropfx2.c: In function 'fatal': +dropfx2.c:2216:6: warning: old-style function definition [-Wold-style-definition] + 2216 | void fatal(msg) + | ^~~~~ nmgetlib.c: In function 'gcg_ranlib': nmgetlib.c:1634:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1634 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); @@ -624,80 +750,6 @@ nmgetlib.c:1674:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1674 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c: In function 'ncbl2_ranlib': -ncbl2_mlib.c:1720:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1720 | fread(str,(size_t)1,(size_t)(llen),m_fd->hfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c:1735:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1735 | fread(my_buff,(size_t)1,llen,m_fd->hfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST dropfx2.c -o drop_tfx.o -ncbl2_mlib.c: In function 'src_int4_read': -ncbl2_mlib.c:1841:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1841 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c: In function 'src_long4_read': -ncbl2_mlib.c:1856:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1856 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c: In function 'src_uint4_read': -ncbl2_mlib.c:1869:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1869 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c: In function 'src_long8_read': -ncbl2_mlib.c:1884:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1884 | fread((char *)&b[0],(size_t)1,(size_t)8,fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c: In function 'ncbi_long8_read': -ncbl2_mlib.c:1904:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1904 | fread((char *)&b[0],(size_t)1,(size_t)8,fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c: In function 'src_char_read': -ncbl2_mlib.c:1911:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1911 | fread(val,(size_t)1,(size_t)1,fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ncbl2_mlib.c: In function 'src_fstr_read': -ncbl2_mlib.c:1916:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1916 | fread(val,(size_t)slen,(size_t)1,fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTY initfa.c -o init_fy.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropfz3.c -o drop_fz.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTY -DTFAST initfa.c -o init_tfy.o -initfa.c: In function 'sortbest': -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST dropfz3.c -o drop_tfz.o -initfa.c:2048:6: warning: old-style function definition [-Wold-style-definition] - 2048 | void sortbest (bptr, nbest, irelv) - | ^~~~~~~~ -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS -DTFAST initfa.c -o init_tfs.o -initfa.c: In function 'sortbest': -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST -DFASTS dropfs2.c -o drop_tfs.o -initfa.c:2048:6: warning: old-style function definition [-Wold-style-definition] - 2048 | void sortbest (bptr, nbest, irelv) - | ^~~~~~~~ -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTS -c cal_consf.c -o calcons_tfs.o -dropfs2.c: In function 'kssort': -dropfs2.c:1277:1: warning: old-style function definition [-Wold-style-definition] - 1277 | kssort (v, n) - | ^~~~~~ -dropfs2.c: In function 'kpsort': -dropfs2.c:1297:1: warning: old-style function definition [-Wold-style-definition] - 1297 | kpsort (v, n) - | ^~~~~~ -dropfs2.c: In function 'krsort': -dropfs2.c:1329:1: warning: old-style function definition [-Wold-style-definition] - 1329 | krsort (v, n) - | ^~~~~~ -initfa.c: In function 'sortbest': -initfa.c:2070:6: warning: old-style function definition [-Wold-style-definition] - 2070 | void sortbest (bptr, nbest, irelv) - | ^~~~~~~~ -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM initfa.c -o init_fm.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM tatstats.c -o tatstats_fm.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM dropfs2.c -o drop_fm.o -initfa.c: In function 'sortbest': -initfa.c:2048:6: warning: old-style function definition [-Wold-style-definition] - 2048 | void sortbest (bptr, nbest, irelv) - | ^~~~~~~~ dropfx2.c: In function 'pro_dna': dropfx2.c:1528:18: warning: passing argument 9 of 'global' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 1528 | dna_prot_seq, prot_seq, 0, 0, &up, &down, &tp, @@ -711,39 +763,13 @@ dropfx2.c:1476:133: note: expected 'unsigned char *' but argument is of type 'const unsigned char *' 1476 | static match_ptr global(int x, int y, int ex, int ey, int **wgts, int gop, int gext, int shift, unsigned char *dnap, unsigned char *pro, int N1, int N2, st_ptr *up_stp, st_ptr *dn_stp, st_ptr *tp_stp, struct smgl_str *smgl_sp); | ~~~~~~~~~~~~~~~^~~ -dropfx2.c: In function 'fatal': -dropfx2.c:2216:6: warning: old-style function definition [-Wold-style-definition] - 2216 | void fatal(msg) - | ^~~~~ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM dropfs2.c -o drop_fm.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTM -c cal_consf.c -o calcons_fm.o -dropfx2.c: In function 'pro_dna': -initfa.c: In function 'sortbest': -dropfz3.c: In function 'kssort': -dropfx2.c:1528:18: warning: passing argument 9 of 'global' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] - 1528 | dna_prot_seq, prot_seq, 0, 0, &up, &down, &tp, - | ^~~~~~~~~~~~ -initfa.c:2048:6: warning: old-style function definition [-Wold-style-definition] - 2048 | void sortbest (bptr, nbest, irelv) - | ^~~~~~~~ -dropfx2.c:1476:112: note: expected 'unsigned char *' but argument is of type 'const unsigned char *' - 1476 | static match_ptr global(int x, int y, int ex, int ey, int **wgts, int gop, int gext, int shift, unsigned char *dnap, unsigned char *pro, int N1, int N2, st_ptr *up_stp, st_ptr *dn_stp, st_ptr *tp_stp, struct smgl_str *smgl_sp); - | ~~~~~~~~~~~~~~~^~~~ -dropfx2.c:1528:32: warning: passing argument 10 of 'global' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] - 1528 | dna_prot_seq, prot_seq, 0, 0, &up, &down, &tp, - | ^~~~~~~~ -dropfx2.c:1476:133: note: expected 'unsigned char *' but argument is of type 'const unsigned char *' - 1476 | static match_ptr global(int x, int y, int ex, int ey, int **wgts, int gop, int gext, int shift, unsigned char *dnap, unsigned char *pro, int N1, int N2, st_ptr *up_stp, st_ptr *dn_stp, st_ptr *tp_stp, struct smgl_str *smgl_sp); - | ~~~~~~~~~~~~~~~^~~ -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c mshowalign2.c -o mshowalign2_s.o -dropfz3.c:1333:1: warning: old-style function definition [-Wold-style-definition] - 1333 | kssort (v, n) - | ^~~~~~ dropfz3.c: In function 'kssort': dropfz3.c:1333:1: warning: old-style function definition [-Wold-style-definition] 1333 | kssort (v, n) | ^~~~~~ dropfz3.c: In function 'pro_dna': -dropfz3.c: In function 'pro_dna': dropfz3.c:1646:18: warning: passing argument 8 of 'global' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 1646 | dna_prot_seq, prot_seq, | ^~~~~~~~~~~~ @@ -760,6 +786,25 @@ dropfx2.c:2216:6: warning: old-style function definition [-Wold-style-definition] 2216 | void fatal(msg) | ^~~~~ +dropfz3.c: In function 'fatal': +dropfz3.c:2280:1: warning: old-style function definition [-Wold-style-definition] + 2280 | fatal(msg) + | ^~~~~ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c mshowalign2.c -o mshowalign2_s.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM -DTFAST initfa.c -o init_tfm.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST -DFASTM dropfs2.c -o drop_tfm.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTM -c cal_consf.c -o calcons_tfm.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF initfa.c -o init_ff.o +dropfz3.c: In function 'kssort': +dropfz3.c:1333:1: warning: old-style function definition [-Wold-style-definition] + 1333 | kssort (v, n) + | ^~~~~~ +initfa.c: In function 'sortbest': +initfa.c:2048:6: warning: old-style function definition [-Wold-style-definition] + 2048 | void sortbest (bptr, nbest, irelv) + | ^~~~~~~~ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTF -c scaleswt.c -o scaleswtf.o +dropfz3.c: In function 'pro_dna': dropfz3.c:1646:18: warning: passing argument 8 of 'global' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 1646 | dna_prot_seq, prot_seq, | ^~~~~~~~~~~~ @@ -772,24 +817,16 @@ dropfz3.c:1601:122: note: expected 'unsigned char *' but argument is of type 'const unsigned char *' 1601 | static match_ptr global(int x, int y, int ex, int ey, int **wgts, int gop, int gext, unsigned char *dnap, unsigned char *pro, int N1, int N2, struct f_struct *f_str); | ~~~~~~~~~~~~~~~^~~ -dropfz3.c: In function 'fatal': -dropfz3.c:2280:1: warning: old-style function definition [-Wold-style-definition] - 2280 | fatal(msg) - | ^~~~~ -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM -DTFAST initfa.c -o init_tfm.o -dropfz3.c: In function 'fatal': -dropfz3.c:2280:1: warning: old-style function definition [-Wold-style-definition] - 2280 | fatal(msg) - | ^~~~~ -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST -DFASTM dropfs2.c -o drop_tfm.o initfa.c: In function 'sortbest': initfa.c:2070:6: warning: old-style function definition [-Wold-style-definition] 2070 | void sortbest (bptr, nbest, irelv) | ^~~~~~~~ -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTM -c cal_consf.c -o calcons_tfm.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF initfa.c -o init_ff.o +dropfz3.c: In function 'fatal': +dropfz3.c:2280:1: warning: old-style function definition [-Wold-style-definition] + 2280 | fatal(msg) + | ^~~~~ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF tatstats.c -o tatstats_ff.o dropfs2.c: In function 'kssort': -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTF -c scaleswt.c -o scaleswtf.o dropfs2.c:1277:1: warning: old-style function definition [-Wold-style-definition] 1277 | kssort (v, n) | ^~~~~~ @@ -801,50 +838,23 @@ dropfs2.c:1329:1: warning: old-style function definition [-Wold-style-definition] 1329 | krsort (v, n) | ^~~~~~ -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF tatstats.c -o tatstats_ff.o initfa.c: In function 'sortbest': initfa.c:2048:6: warning: old-style function definition [-Wold-style-definition] 2048 | void sortbest (bptr, nbest, irelv) | ^~~~~~~~ -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF dropff2.c -o drop_ff2.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTF -c cal_consf.c -o calcons_ff.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF -DTFAST initfa.c -o init_tf.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF -DTFAST dropff2.c -o drop_tff.o -initfa.c: In function 'sortbest': -initfa.c:2070:6: warning: old-style function definition [-Wold-style-definition] - 2070 | void sortbest (bptr, nbest, irelv) - | ^~~~~~~~ dropfs2.c: In function 'kssort': -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTF -c cal_consf.c -o calcons_tff.o -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DNORMAL_DIST -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c scaleswn.c -o scale_sn.o -dropfs2.c: In function 'kssort': -initfa.c: In function 'sortbest': -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DGLSEARCH initfa.c -o init_lnw_sse.o -initfa.c: In function 'sortbest': -initfa.c: In function 'sortbest': -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DSW_SSE2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnnw2.c -o droplnw_sse.o -dropff2.c: In function 'savemax': dropfs2.c:1277:1: warning: old-style function definition [-Wold-style-definition] 1277 | kssort (v, n) | ^~~~~~ -initfa.c:2070:6: warning: old-style function definition [-Wold-style-definition] - 2070 | void sortbest (bptr, nbest, irelv) - | ^~~~~~~~ -dropff2.c:697:1: warning: old-style function definition [-Wold-style-definition] - 697 | savemax (dptr, f_str) - | ^~~~~~~ dropfs2.c: In function 'kpsort': dropfs2.c:1297:1: warning: old-style function definition [-Wold-style-definition] 1297 | kpsort (v, n) | ^~~~~~ -initfa.c:2070:6: warning: old-style function definition [-Wold-style-definition] - 2070 | void sortbest (bptr, nbest, irelv) - | ^~~~~~~~ dropfs2.c: In function 'krsort': dropfs2.c:1329:1: warning: old-style function definition [-Wold-style-definition] 1329 | krsort (v, n) | ^~~~~~ -dropff2.c: In function 'kpsort': +dropfs2.c: In function 'kssort': dropfs2.c:1277:1: warning: old-style function definition [-Wold-style-definition] 1277 | kssort (v, n) | ^~~~~~ @@ -856,19 +866,36 @@ dropfs2.c:1329:1: warning: old-style function definition [-Wold-style-definition] 1329 | krsort (v, n) | ^~~~~~ -dropff2.c:1118:1: warning: old-style function definition [-Wold-style-definition] - 1118 | kpsort (v, n) - | ^~~~~~ -dropff2.c: In function 'krsort': -dropff2.c:1140:1: warning: old-style function definition [-Wold-style-definition] - 1140 | krsort (v, n) - | ^~~~~~ +initfa.c: In function 'sortbest': +initfa.c:2070:6: warning: old-style function definition [-Wold-style-definition] + 2070 | void sortbest (bptr, nbest, irelv) + | ^~~~~~~~ +initfa.c: In function 'sortbest': +initfa.c:2070:6: warning: old-style function definition [-Wold-style-definition] + 2070 | void sortbest (bptr, nbest, irelv) + | ^~~~~~~~ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF dropff2.c -o drop_ff2.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTF -c cal_consf.c -o calcons_ff.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF -DTFAST initfa.c -o init_tf.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF -DTFAST dropff2.c -o drop_tff.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTF -c cal_consf.c -o calcons_tff.o +initfa.c: In function 'sortbest': +initfa.c:2070:6: warning: old-style function definition [-Wold-style-definition] + 2070 | void sortbest (bptr, nbest, irelv) + | ^~~~~~~~ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DNORMAL_DIST -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c scaleswn.c -o scale_sn.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DGLSEARCH initfa.c -o init_lnw_sse.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DSW_SSE2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnnw2.c -o droplnw_sse.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c glocal_sse2.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DGGSEARCH -c wm_align.c -o gwm_align.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DGGSEARCH initfa.c -o init_gnw_sse.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DGLOBAL_GLOBAL -DSW_SSE2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnnw2.c -o dropgnw_sse.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c global_sse2.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -o ../bin/map_db map_db.c +initfa.c: In function 'sortbest': +initfa.c:2070:6: warning: old-style function definition [-Wold-style-definition] + 2070 | void sortbest (bptr, nbest, irelv) + | ^~~~~~~~ dropff2.c: In function 'savemax': dropff2.c:697:1: warning: old-style function definition [-Wold-style-definition] 697 | savemax (dptr, f_str) @@ -881,18 +908,10 @@ dropff2.c:1140:1: warning: old-style function definition [-Wold-style-definition] 1140 | krsort (v, n) | ^~~~~~ -initfa.c: In function 'sortbest': -initfa.c:2048:6: warning: old-style function definition [-Wold-style-definition] - 2048 | void sortbest (bptr, nbest, irelv) - | ^~~~~~~~ -initfa.c:2070:6: warning: old-style function definition [-Wold-style-definition] - 2070 | void sortbest (bptr, nbest, irelv) - | ^~~~~~~~ map_db.c: In function 'main': map_db.c:151:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 151 | fgets(lname,sizeof(lname),stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -lpthread map_db.c: In function 'gbf_get_ent': map_db.c:514:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 514 | fgets(lline,MAXLINE,libf); @@ -905,14 +924,37 @@ initfa.c:2048:6: warning: old-style function definition [-Wold-style-definition] 2048 | void sortbest (bptr, nbest, irelv) | ^~~~~~~~ +initfa.c: In function 'sortbest': +initfa.c:2048:6: warning: old-style function definition [-Wold-style-definition] + 2048 | void sortbest (bptr, nbest, irelv) + | ^~~~~~~~ +dropff2.c: In function 'savemax': +dropff2.c:697:1: warning: old-style function definition [-Wold-style-definition] + 697 | savemax (dptr, f_str) + | ^~~~~~~ +dropff2.c: In function 'kpsort': +dropff2.c:1118:1: warning: old-style function definition [-Wold-style-definition] + 1118 | kpsort (v, n) + | ^~~~~~ +dropff2.c: In function 'krsort': +dropff2.c:1140:1: warning: old-style function definition [-Wold-style-definition] + 1140 | krsort (v, n) + | ^~~~~~ +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 -lpthread 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_sse.o dropgsw2_sse.o smith_waterman_sse2.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 -lpthread 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 -lpthread 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 -lpthread 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 -lpthread 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 -lpthread +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 -lpthread +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 -lpthread +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 -lpthread +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 -lpthread +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 -lpthread 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 -lpthread +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_sse.o droplnw_sse.o glocal_sse2.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 -lpthread +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_sse.o dropgnw_sse.o global_sse2.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 -lpthread 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_sse.o smith_waterman_sse2.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 -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 -lpthread compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -1042,9 +1084,6 @@ mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ -compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] - 959 | re_openlib(struct lmf_str *, int outtty); - | ^ compacc2e.c:2313:1: note: type mismatch in parameter 1 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ @@ -1089,6 +1128,9 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used +compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] + 959 | re_openlib(struct lmf_str *, int outtty); + | ^ nmgetlib.c:514:3: note: type mismatch in parameter 2 514 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ @@ -1097,6 +1139,9 @@ compacc2e.c:69:13: warning: type of 'qshuffle' does not match original declaration [-Wlto-type-mismatch] 69 | extern void qshuffle(unsigned char *aa0, int n0, int nm0, void *); | ^ +compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] + 959 | re_openlib(struct lmf_str *, int outtty); + | ^ initfa.c:2032:1: note: type mismatch in parameter 1 2032 | qshuffle() {} | ^ @@ -1104,12 +1149,20 @@ mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ +nmgetlib.c:514:3: note: type mismatch in parameter 2 + 514 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) + | ^ +nmgetlib.c:514:3: note: 're_openlib' was previously declared here +nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used compacc2e.c:2313:1: note: type mismatch in parameter 1 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2313:1: note: type 'long int' should match type 'int' compacc2e.c:2313:1: note: 's_annot_to_aa1a' was previously declared here compacc2e.c:2313:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used +compacc2e.c:69:13: warning: type of 'qshuffle' does not match original declaration [-Wlto-type-mismatch] + 69 | extern void qshuffle(unsigned char *aa0, int n0, int nm0, void *); + | ^ comp_lib9.c:88:7: warning: type of 'my_srand' does not match original declaration [-Wlto-type-mismatch] 88 | void *my_srand(); | ^ @@ -1121,12 +1174,19 @@ comp_lib9.c:244:6: warning: type of 'last_stats' does not match original declaration [-Wlto-type-mismatch] 244 | void last_stats(const unsigned char *, int, | ^ -compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] - 959 | re_openlib(struct lmf_str *, int outtty); +initfa.c:2032:1: note: type mismatch in parameter 1 + 2032 | qshuffle() {} + | ^ +initfa.c:2032:1: note: 'qshuffle' was previously declared here +mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] + 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ scaleswn.c:2931:6: note: type mismatch in parameter 1 2931 | void last_stats() {} | ^ +compacc2e.c:2313:1: note: type mismatch in parameter 1 + 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { + | ^ scaleswn.c:2931:6: note: 'last_stats' was previously declared here comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, @@ -1135,23 +1195,18 @@ 2036 | last_calc( | ^ initfa.c:2036:1: note: 'last_calc' was previously declared here -nmgetlib.c:514:3: note: type mismatch in parameter 2 - 514 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) - | ^ -nmgetlib.c:514:3: note: 're_openlib' was previously declared here +compacc2e.c:2313:1: note: type 'long int' should match type 'int' mshowbest.c:84:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch] 84 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ -nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used compacc2e.c:2202:1: note: type mismatch in parameter 4 2202 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2202:1: note: type 'long int' should match type 'int' compacc2e.c:2202:1: note: 'get_annot' was previously declared here compacc2e.c:2202:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used -compacc2e.c:69:13: warning: type of 'qshuffle' does not match original declaration [-Wlto-type-mismatch] - 69 | extern void qshuffle(unsigned char *aa0, int n0, int nm0, void *); - | ^ +compacc2e.c:2313:1: note: 's_annot_to_aa1a' was previously declared here +compacc2e.c:2313:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ @@ -1159,19 +1214,6 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -initfa.c:2032:1: note: type mismatch in parameter 1 - 2032 | qshuffle() {} - | ^ -initfa.c:2032:1: note: 'qshuffle' was previously declared here -mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] - 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); - | ^ -compacc2e.c:2313:1: note: type mismatch in parameter 1 - 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { - | ^ -compacc2e.c:2313:1: note: type 'long int' should match type 'int' -compacc2e.c:2313:1: note: 's_annot_to_aa1a' was previously declared here -compacc2e.c:2313:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used comp_lib9.c:88:7: warning: type of 'my_srand' does not match original declaration [-Wlto-type-mismatch] 88 | void *my_srand(); | ^ @@ -1213,18 +1255,14 @@ compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ +compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] + 959 | re_openlib(struct lmf_str *, int outtty); + | ^ nmgetlib.c:514:3: note: type mismatch in parameter 2 514 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:514:3: note: 're_openlib' was previously declared here nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used -compacc2e.c:69:13: warning: type of 'qshuffle' does not match original declaration [-Wlto-type-mismatch] - 69 | extern void qshuffle(unsigned char *aa0, int n0, int nm0, void *); - | ^ -initfa.c:2032:1: note: type mismatch in parameter 1 - 2032 | qshuffle() {} - | ^ -initfa.c:2032:1: note: 'qshuffle' was previously declared here mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ @@ -1242,20 +1280,14 @@ | ^ mrandom.c:42:1: note: type 'int' should match type 'void' mrandom.c:42:1: note: 'my_srand' was previously declared here -comp_lib9.c:244:6: warning: type of 'last_stats' does not match original declaration [-Wlto-type-mismatch] - 244 | void last_stats(const unsigned char *, int, - | ^ -scaleswn.c:2931:6: note: type mismatch in parameter 1 - 2931 | void last_stats() {} - | ^ -scaleswn.c:2931:6: note: 'last_stats' was previously declared here -comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] - 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, - | ^ -initfa.c:2036:1: note: type mismatch in parameter 6 - 2036 | last_calc( +comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch] + 236 | process_hist(struct stat_str *sptr, int nstats, | ^ -initfa.c:2036:1: note: 'last_calc' was previously declared here +scaleswt.c:164:1: note: type mismatch in parameter 7 + 164 | process_hist(struct stat_str *sptr, int nstats, + | ^ +scaleswt.c:164:1: note: 'process_hist' was previously declared here +scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used mshowbest.c:84:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch] 84 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ @@ -1272,10 +1304,6 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -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 -lpthread -compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] - 959 | re_openlib(struct lmf_str *, int outtty); - | ^ nmgetlib.c:514:3: note: type mismatch in parameter 2 514 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ @@ -1312,6 +1340,13 @@ 2931 | void last_stats() {} | ^ scaleswn.c:2931:6: note: 'last_stats' was previously declared here +comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] + 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, + | ^ +initfa.c:2036:1: note: type mismatch in parameter 6 + 2036 | last_calc( + | ^ +initfa.c:2036:1: note: 'last_calc' was previously declared here mshowbest.c:84:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch] 84 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ @@ -1328,7 +1363,6 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -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 -lpthread compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -1337,6 +1371,13 @@ | ^ nmgetlib.c:514:3: note: 're_openlib' was previously declared here nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used +compacc2e.c:69:13: warning: type of 'qshuffle' does not match original declaration [-Wlto-type-mismatch] + 69 | extern void qshuffle(unsigned char *aa0, int n0, int nm0, void *); + | ^ +initfa.c:2032:1: note: type mismatch in parameter 1 + 2032 | qshuffle() {} + | ^ +initfa.c:2032:1: note: 'qshuffle' was previously declared here mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ @@ -1344,6 +1385,9 @@ 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2313:1: note: type 'long int' should match type 'int' +compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] + 959 | re_openlib(struct lmf_str *, int outtty); + | ^ compacc2e.c:2313:1: note: 's_annot_to_aa1a' was previously declared here compacc2e.c:2313:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used comp_lib9.c:88:7: warning: type of 'my_srand' does not match original declaration [-Wlto-type-mismatch] @@ -1354,64 +1398,28 @@ | ^ mrandom.c:42:1: note: type 'int' should match type 'void' mrandom.c:42:1: note: 'my_srand' was previously declared here -comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch] - 236 | process_hist(struct stat_str *sptr, int nstats, - | ^ -scaleswt.c:164:1: note: type mismatch in parameter 7 - 164 | process_hist(struct stat_str *sptr, int nstats, - | ^ -scaleswt.c:164:1: note: 'process_hist' was previously declared here -scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used -mshowbest.c:84:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch] - 84 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, - | ^ -compacc2e.c:2202:1: note: type mismatch in parameter 4 - 2202 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, - | ^ -compacc2e.c:2202:1: note: type 'long int' should match type 'int' -compacc2e.c:2202:1: note: 'get_annot' was previously declared here -compacc2e.c:2202:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used -comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch] - 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, - | ^ -mshowalign2.c:134:6: note: 'showalign' was previously declared here - 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, +comp_lib9.c:244:6: warning: type of 'last_stats' does not match original declaration [-Wlto-type-mismatch] + 244 | void last_stats(const unsigned char *, int, | ^ -mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -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 -lpthread compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:514:3: note: type mismatch in parameter 2 514 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ +scaleswn.c:2931:6: note: type mismatch in parameter 1 + 2931 | void last_stats() {} + | ^ +scaleswn.c:2931:6: note: 'last_stats' was previously declared here nmgetlib.c:514:3: note: 're_openlib' was previously declared here -nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used -mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] - 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); - | ^ -compacc2e.c:2313:1: note: type mismatch in parameter 1 - 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { - | ^ -compacc2e.c:2313:1: note: type 'long int' should match type 'int' -compacc2e.c:2313:1: note: 's_annot_to_aa1a' was previously declared here -compacc2e.c:2313:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used -comp_lib9.c:88:7: warning: type of 'my_srand' does not match original declaration [-Wlto-type-mismatch] - 88 | void *my_srand(); - | ^ -mrandom.c:42:1: note: type mismatch in parameter 1 - 42 | my_srand(int set) /* initialize random number generator */ - | ^ -mrandom.c:42:1: note: type 'int' should match type 'void' -mrandom.c:42:1: note: 'my_srand' was previously declared here -comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch] - 236 | process_hist(struct stat_str *sptr, int nstats, - | ^ -scaleswt.c:164:1: note: type mismatch in parameter 7 - 164 | process_hist(struct stat_str *sptr, int nstats, +comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] + 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, + | ^ +initfa.c:2036:1: note: type mismatch in parameter 6 + 2036 | last_calc( | ^ -scaleswt.c:164:1: note: 'process_hist' was previously declared here -scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used +initfa.c:2036:1: note: 'last_calc' was previously declared here +nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used mshowbest.c:84:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch] 84 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ @@ -1424,23 +1432,13 @@ comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ +mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] + 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); + | ^ mshowalign2.c:134:6: note: 'showalign' was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -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_sse.o droplnw_sse.o glocal_sse2.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 -lpthread -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 -lpthread -compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] - 959 | re_openlib(struct lmf_str *, int outtty); - | ^ -nmgetlib.c:514:3: note: type mismatch in parameter 2 - 514 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) - | ^ -nmgetlib.c:514:3: note: 're_openlib' was previously declared here -nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used -mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] - 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); - | ^ compacc2e.c:2313:1: note: type mismatch in parameter 1 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ @@ -1472,13 +1470,6 @@ compacc2e.c:2202:1: note: type 'long int' should match type 'int' compacc2e.c:2202:1: note: 'get_annot' was previously declared here compacc2e.c:2202:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used -mshowalign2.c:85:1: warning: type of 'buf_align_seq' does not match original declaration [-Wlto-type-mismatch] - 85 | buf_align_seq(unsigned char **aa0, int n0, - | ^ -compacc2e.c:3597:1: note: type mismatch in parameter 8 - 3597 | buf_align_seq(unsigned char **aa0, int n0, - | ^ -compacc2e.c:3597:1: note: 'buf_align_seq' was previously declared here comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ @@ -1486,20 +1477,28 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] - 959 | re_openlib(struct lmf_str *, int outtty); - | ^ nmgetlib.c:514:3: note: type mismatch in parameter 2 514 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:514:3: note: 're_openlib' was previously declared here nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used +compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] + 959 | re_openlib(struct lmf_str *, int outtty); + | ^ mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ +nmgetlib.c:514:3: note: type mismatch in parameter 2 + 514 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) + | ^ +nmgetlib.c:514:3: note: 're_openlib' was previously declared here +nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used compacc2e.c:2313:1: note: type mismatch in parameter 1 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ +compacc2e.c:69:13: warning: type of 'qshuffle' does not match original declaration [-Wlto-type-mismatch] + 69 | extern void qshuffle(unsigned char *aa0, int n0, int nm0, void *); + | ^ compacc2e.c:2313:1: note: type 'long int' should match type 'int' compacc2e.c:2313:1: note: 's_annot_to_aa1a' was previously declared here compacc2e.c:2313:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used @@ -1511,15 +1510,19 @@ | ^ mrandom.c:42:1: note: type 'int' should match type 'void' mrandom.c:42:1: note: 'my_srand' was previously declared here +initfa.c:2032:1: note: type mismatch in parameter 1 + 2032 | qshuffle() {} + | ^ +initfa.c:2032:1: note: 'qshuffle' was previously declared here comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch] 236 | process_hist(struct stat_str *sptr, int nstats, | ^ +mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] + 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); + | ^ scaleswt.c:164:1: note: type mismatch in parameter 7 164 | process_hist(struct stat_str *sptr, int nstats, | ^ -compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] - 959 | re_openlib(struct lmf_str *, int outtty); - | ^ scaleswt.c:164:1: note: 'process_hist' was previously declared here scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used mshowbest.c:84:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch] @@ -1531,27 +1534,19 @@ compacc2e.c:2202:1: note: type 'long int' should match type 'int' compacc2e.c:2202:1: note: 'get_annot' was previously declared here compacc2e.c:2202:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used -nmgetlib.c:514:3: note: type mismatch in parameter 2 - 514 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) - | ^ +compacc2e.c:2313:1: note: type mismatch in parameter 1 + 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { + | ^ comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ -nmgetlib.c:514:3: note: 're_openlib' was previously declared here -nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used +compacc2e.c:2313:1: note: type 'long int' should match type 'int' +compacc2e.c:2313:1: note: 's_annot_to_aa1a' was previously declared here +compacc2e.c:2313:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used mshowalign2.c:134:6: note: 'showalign' was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ -mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] - 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); - | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -compacc2e.c:2313:1: note: type mismatch in parameter 1 - 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { - | ^ -compacc2e.c:2313:1: note: type 'long int' should match type 'int' -compacc2e.c:2313:1: note: 's_annot_to_aa1a' was previously declared here -compacc2e.c:2313:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used comp_lib9.c:88:7: warning: type of 'my_srand' does not match original declaration [-Wlto-type-mismatch] 88 | void *my_srand(); | ^ @@ -1560,14 +1555,20 @@ | ^ mrandom.c:42:1: note: type 'int' should match type 'void' mrandom.c:42:1: note: 'my_srand' was previously declared here -comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch] - 236 | process_hist(struct stat_str *sptr, int nstats, - | ^ -scaleswt.c:164:1: note: type mismatch in parameter 7 - 164 | process_hist(struct stat_str *sptr, int nstats, +comp_lib9.c:244:6: warning: type of 'last_stats' does not match original declaration [-Wlto-type-mismatch] + 244 | void last_stats(const unsigned char *, int, + | ^ +scaleswn.c:2931:6: note: type mismatch in parameter 1 + 2931 | void last_stats() {} + | ^ +scaleswn.c:2931:6: note: 'last_stats' was previously declared here +comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] + 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, + | ^ +initfa.c:2036:1: note: type mismatch in parameter 6 + 2036 | last_calc( | ^ -scaleswt.c:164:1: note: 'process_hist' was previously declared here -scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used +initfa.c:2036:1: note: 'last_calc' was previously declared here mshowbest.c:84:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch] 84 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ @@ -1584,7 +1585,6 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -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_sse.o dropgnw_sse.o global_sse2.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 -lpthread compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 959 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -1655,13 +1655,6 @@ | ^ nmgetlib.c:514:3: note: 're_openlib' was previously declared here nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used -compacc2e.c:69:13: warning: type of 'qshuffle' does not match original declaration [-Wlto-type-mismatch] - 69 | extern void qshuffle(unsigned char *aa0, int n0, int nm0, void *); - | ^ -initfa.c:2032:1: note: type mismatch in parameter 1 - 2032 | qshuffle() {} - | ^ -initfa.c:2032:1: note: 'qshuffle' was previously declared here mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ @@ -1679,20 +1672,14 @@ | ^ mrandom.c:42:1: note: type 'int' should match type 'void' mrandom.c:42:1: note: 'my_srand' was previously declared here -comp_lib9.c:244:6: warning: type of 'last_stats' does not match original declaration [-Wlto-type-mismatch] - 244 | void last_stats(const unsigned char *, int, - | ^ -scaleswn.c:2931:6: note: type mismatch in parameter 1 - 2931 | void last_stats() {} - | ^ -scaleswn.c:2931:6: note: 'last_stats' was previously declared here -comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] - 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, - | ^ -initfa.c:2036:1: note: type mismatch in parameter 6 - 2036 | last_calc( +comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch] + 236 | process_hist(struct stat_str *sptr, int nstats, | ^ -initfa.c:2036:1: note: 'last_calc' was previously declared here +scaleswt.c:164:1: note: type mismatch in parameter 7 + 164 | process_hist(struct stat_str *sptr, int nstats, + | ^ +scaleswt.c:164:1: note: 'process_hist' was previously declared here +scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used mshowbest.c:84:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch] 84 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ @@ -1702,6 +1689,13 @@ compacc2e.c:2202:1: note: type 'long int' should match type 'int' compacc2e.c:2202:1: note: 'get_annot' was previously declared here compacc2e.c:2202:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used +mshowalign2.c:85:1: warning: type of 'buf_align_seq' does not match original declaration [-Wlto-type-mismatch] + 85 | buf_align_seq(unsigned char **aa0, int n0, + | ^ +compacc2e.c:3597:1: note: type mismatch in parameter 8 + 3597 | buf_align_seq(unsigned char **aa0, int n0, + | ^ +compacc2e.c:3597:1: note: 'buf_align_seq' was previously declared here comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ @@ -1717,6 +1711,23 @@ | ^ nmgetlib.c:514:3: note: 're_openlib' was previously declared here nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used +mshowbest.c:62:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] + 62 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); + | ^ +compacc2e.c:2313:1: note: type mismatch in parameter 1 + 2313 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { + | ^ +compacc2e.c:2313:1: note: type 'long int' should match type 'int' +compacc2e.c:2313:1: note: 's_annot_to_aa1a' was previously declared here +compacc2e.c:2313:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used +compacc2e.c:959:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] + 959 | re_openlib(struct lmf_str *, int outtty); + | ^ +nmgetlib.c:514:3: note: type mismatch in parameter 2 + 514 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) + | ^ +nmgetlib.c:514:3: note: 're_openlib' was previously declared here +nmgetlib.c:514:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used compacc2e.c:69:13: warning: type of 'qshuffle' does not match original declaration [-Wlto-type-mismatch] 69 | extern void qshuffle(unsigned char *aa0, int n0, int nm0, void *); | ^ @@ -1748,13 +1759,38 @@ 2931 | void last_stats() {} | ^ scaleswn.c:2931:6: note: 'last_stats' was previously declared here -comp_lib9.c:250:5: warning: type of 'last_calc' does not match original declaration [-Wlto-type-mismatch] - 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, - | ^ -initfa.c:2036:1: note: type mismatch in parameter 6 - 2036 | last_calc( +mshowbest.c:84:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch] + 84 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ -initfa.c:2036:1: note: 'last_calc' was previously declared here +compacc2e.c:2202:1: note: type mismatch in parameter 4 + 2202 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, + | ^ +compacc2e.c:2202:1: note: type 'long int' should match type 'int' +compacc2e.c:2202:1: note: 'get_annot' was previously declared here +compacc2e.c:2202:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used +comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch] + 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, + | ^ +mshowalign2.c:134:6: note: 'showalign' was previously declared here + 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, + | ^ +mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used +comp_lib9.c:88:7: warning: type of 'my_srand' does not match original declaration [-Wlto-type-mismatch] + 88 | void *my_srand(); + | ^ +mrandom.c:42:1: note: type mismatch in parameter 1 + 42 | my_srand(int set) /* initialize random number generator */ + | ^ +mrandom.c:42:1: note: type 'int' should match type 'void' +mrandom.c:42:1: note: 'my_srand' was previously declared here +comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch] + 236 | process_hist(struct stat_str *sptr, int nstats, + | ^ +scaleswt.c:164:1: note: type mismatch in parameter 7 + 164 | process_hist(struct stat_str *sptr, int nstats, + | ^ +scaleswt.c:164:1: note: 'process_hist' was previously declared here +scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used mshowbest.c:84:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch] 84 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ @@ -1806,21 +1842,21 @@ make[1]: Entering directory '/build/reproducible-path/fasta3-36.3.8i.14-Nov-2020' cd test ; ./test2G.sh && ./test.sh && ../bin/fasta36 -q ../seq/mgstm1.aa ../seq/prot_test.lseg -STARTING FASTA36 Wed Sep 24 13:47:52 2025 on ionos11-amd64 -Linux ionos11-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux +STARTING FASTA36 Tue Oct 27 20:17:27 2026 on i-capture-the-hostname +Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux -starting prss36(ssearch/fastx) Wed Sep 24 13:47:52 2025 +starting prss36(ssearch/fastx) Tue Oct 27 20:17:27 2026 done -starting lalign36 Wed Sep 24 13:47:52 2025 -FINISHED Wed Sep 24 13:48:22 2025 +starting lalign36 Tue Oct 27 20:17:27 2026 +FINISHED Tue Oct 27 20:18:20 2026 -STARTING FASTA36 Wed Sep 24 13:48:22 2025 on ionos11-amd64 -Linux ionos11-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux +STARTING FASTA36 Tue Oct 27 20:18:20 2026 on i-capture-the-hostname +Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux -starting prss36(ssearch/fastx) Wed Sep 24 13:48:22 2025 +starting prss36(ssearch/fastx) Tue Oct 27 20:18:20 2026 done -starting lalign36 Wed Sep 24 13:48:22 2025 -FINISHED Wed Sep 24 13:48:58 2025 +starting lalign36 Tue Oct 27 20:18:22 2026 +FINISHED Tue Oct 27 20:19:18 2026 # ../bin/fasta36 -q ../seq/mgstm1.aa ../seq/prot_test.lseg FASTA searches a protein or DNA sequence data bank version 36.3.8i Nov, 2022 @@ -1832,27 +1868,27 @@ Library: ../seq/prot_test.lseg 2267 residues in 12 sequences -Statistics: (shuffled [143]) MLE statistics: Lambda= 0.1407; K=0.01047 - statistics sampled from 4 (4) to 143 sequences +Statistics: (shuffled [136]) MLE statistics: Lambda= 0.1293; K=0.00743 + statistics sampled from 4 (4) to 136 sequences Algorithm: FASTA (3.8 Nov 2011) [optimized] Parameters: BL50 matrix (15:-5), open/ext: -10/-2 ktup: 2, E-join: 1 (0.667), E-opt: 0.2 (0.333), width: 16 - Scan time: 0.010 + Scan time: 0.040 The best scores are: opt bits E(12) -sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 260.5 2.2e-73 -sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 56.5 5.7e-12 -sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 18.7 0.82 -sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 17.1 5 -sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 15.7 5.2 -sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 14.7 7.1 -sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 14.5 7.6 -sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 14.5 9.4 -sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 12.9 9.6 -sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 13.7 9.6 +sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 240.6 2.2e-67 +sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 53.2 5.8e-11 +sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 18.5 0.98 +sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 15.7 5.3 +sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 17.0 5.4 +sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 14.7 6.9 +sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 14.5 7.4 +sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 13.1 9 +sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 13.8 9.2 +sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 14.5 9.2 >>sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 O (218 aa) - initn: 1242 init1: 1242 opt: 1242 Z-score: 1369.2 bits: 260.5 E(12): 2.2e-73 + initn: 1242 init1: 1242 opt: 1242 Z-score: 1261.7 bits: 240.6 E(12): 2.2e-67 Smith-Waterman score: 1242; 78.0% identity (95.4% similar) in 218 aa overlap (1-218:1-218) 10 20 30 40 50 60 @@ -1880,7 +1916,7 @@ 190 200 210 >>sp|P00502|GSTA1_RAT Glutathione S-transferase alpha-1 (222 aa) - initn: 204 init1: 73 opt: 237 Z-score: 266.7 bits: 56.5 E(12): 5.7e-12 + initn: 204 init1: 73 opt: 237 Z-score: 248.6 bits: 53.2 E(12): 5.8e-11 Smith-Waterman score: 237; 27.4% identity (57.0% similar) in 223 aa overlap (4-218:6-218) 10 20 30 40 50 @@ -1908,7 +1944,7 @@ 180 190 200 210 220 >>sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Homo s (142 aa) - initn: 40 init1: 40 opt: 51 Z-score: 66.1 bits: 18.7 E(12): 0.82 + initn: 40 init1: 40 opt: 51 Z-score: 64.7 bits: 18.5 E(12): 0.98 Smith-Waterman score: 51; 25.6% identity (69.2% similar) in 39 aa overlap (177-214:36-73) 150 160 170 180 190 200 @@ -1923,8 +1959,24 @@ sp|P69 DALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHA 70 80 90 100 110 120 +>>sp|P14960|RBS_GUITH Ribulose bisphosphate carboxylase (139 aa) + initn: 56 init1: 36 opt: 36 Z-score: 49.7 bits: 15.7 E(12): 5.3 +Smith-Waterman score: 36; 57.1% identity (85.7% similar) in 7 aa overlap (7-13:47-53) + + 10 20 30 +sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMG + ::.. :: +sp|P14 EQIVKQIQYAISKNWALNVEWTDDPHPRNAYWDLWGLPLFGIKDPAAVMFEINACRKAKP + 20 30 40 50 60 70 + + 40 50 60 70 80 90 +sp|P10 DAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIR + +sp|P14 ACYVKVNAFDNSRGVESCCLSFIVQRPTSNEPGFQLIRSEVDSRNIRYTIQSYASTRPEG + 80 90 100 110 120 130 + >>sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinase ca (351 aa) - initn: 43 init1: 43 opt: 43 Z-score: 50.3 bits: 17.1 E(12): 5 + initn: 43 init1: 43 opt: 43 Z-score: 49.5 bits: 17.0 E(12): 5.4 Smith-Waterman score: 54; 23.6% identity (47.2% similar) in 72 aa overlap (137-206:229-300) 110 120 130 140 150 160 @@ -1942,24 +1994,8 @@ sp|P00 FKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF 320 330 340 350 ->>sp|P14960|RBS_GUITH Ribulose bisphosphate carboxylase (139 aa) - initn: 56 init1: 36 opt: 36 Z-score: 49.9 bits: 15.7 E(12): 5.2 -Smith-Waterman score: 36; 57.1% identity (85.7% similar) in 7 aa overlap (7-13:47-53) - - 10 20 30 -sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMG - ::.. :: -sp|P14 EQIVKQIQYAISKNWALNVEWTDDPHPRNAYWDLWGLPLFGIKDPAAVMFEINACRKAKP - 20 30 40 50 60 70 - - 40 50 60 70 80 90 -sp|P10 DAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIR - -sp|P14 ACYVKVNAFDNSRGVESCCLSFIVQRPTSNEPGFQLIRSEVDSRNIRYTIQSYASTRPEG - 80 90 100 110 120 130 - >>sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG OS= (108 aa) - initn: 31 init1: 31 opt: 31 Z-score: 46.3 bits: 14.7 E(12): 7.1 + initn: 31 init1: 31 opt: 31 Z-score: 46.6 bits: 14.7 E(12): 6.9 Smith-Waterman score: 33; 36.0% identity (54.0% similar) in 50 aa overlap (150-190:16-64) 120 130 140 150 160 170 @@ -1975,7 +2011,7 @@ 50 60 70 80 90 100 >>sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodytes GN (105 aa) - initn: 30 init1: 30 opt: 30 Z-score: 45.5 bits: 14.5 E(12): 7.6 + initn: 30 init1: 30 opt: 30 Z-score: 45.9 bits: 14.5 E(12): 7.4 Smith-Waterman score: 36; 26.5% identity (54.4% similar) in 68 aa overlap (129-193:28-88) 100 110 120 130 140 150 @@ -1993,24 +2029,8 @@ sp|P10 SNK ->>sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle OS=H (160 aa) - initn: 30 init1: 30 opt: 30 Z-score: 42.2 bits: 14.5 E(12): 9.4 -Smith-Waterman score: 41; 25.9% identity (63.0% similar) in 54 aa overlap (44-92:13-62) - - 20 30 40 50 60 70 -sp|P10 THPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKIT-- - :. . .:: ..:. . ::. :. -sp|P02 MTDQQAEARSYLSEEMIAEFKAAFDM----FDADGGGDISVK - 10 20 30 - - 80 90 100 110 120 -sp|P10 QSNAILRYLAR---KHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFL - . ....:.:.. :..::. :: -sp|P02 ELGTVMRMLGQTPTKEELDAIIEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELAE - 40 50 60 70 80 90 - >>sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococcus a (54 aa) - initn: 22 init1: 22 opt: 22 Z-score: 41.9 bits: 12.9 E(12): 9.6 + initn: 22 init1: 22 opt: 22 Z-score: 43.0 bits: 13.1 E(12): 9 Smith-Waterman score: 25; 50.0% identity (100.0% similar) in 4 aa overlap (171-174:15-18) 150 160 170 180 190 200 @@ -2026,7 +2046,7 @@ 50 >>sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A31 O (95 aa) - initn: 26 init1: 26 opt: 26 Z-score: 41.9 bits: 13.7 E(12): 9.6 + initn: 26 init1: 26 opt: 26 Z-score: 42.6 bits: 13.8 E(12): 9.2 Smith-Waterman score: 30; 54.5% identity (63.6% similar) in 11 aa overlap (115-125:86-94) 90 100 110 120 130 140 @@ -2038,13 +2058,29 @@ 150 160 170 180 190 200 sp|P10 RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYI +>>sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle OS=H (160 aa) + initn: 30 init1: 30 opt: 30 Z-score: 42.6 bits: 14.5 E(12): 9.2 +Smith-Waterman score: 41; 25.9% identity (63.0% similar) in 54 aa overlap (44-92:13-62) + + 20 30 40 50 60 70 +sp|P10 THPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKIT-- + :. . .:: ..:. . ::. :. +sp|P02 MTDQQAEARSYLSEEMIAEFKAAFDM----FDADGGGDISVK + 10 20 30 + + 80 90 100 110 120 +sp|P10 QSNAILRYLAR---KHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFL + . ....:.:.. :..::. :: +sp|P02 ELGTVMRMLGQTPTKEELDAIIEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELAE + 40 50 60 70 80 90 + 218 residues in 1 query sequences 2267 residues in 12 library sequences Tcomplib [36.3.8i Nov, 2022] (128 proc in memory [0G]) - start: Wed Sep 24 13:48:58 2025 done: Wed Sep 24 13:48:58 2025 - Total Scan time: 0.010 Total Display time: 0.030 + start: Tue Oct 27 20:19:18 2026 done: Tue Oct 27 20:19:18 2026 + Total Scan time: 0.040 Total Display time: 0.040 Function used was FASTA [36.3.8i Nov, 2022] rm -rf test/results/test* @@ -2076,8 +2112,8 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'fasta3-doc' in '../fasta3-doc_36.3.8i.14-Nov-2020-4_all.deb'. dpkg-deb: building package 'fasta3-dbgsym' in '../fasta3-dbgsym_36.3.8i.14-Nov-2020-4_amd64.deb'. +dpkg-deb: building package 'fasta3-doc' in '../fasta3-doc_36.3.8i.14-Nov-2020-4_all.deb'. dpkg-deb: building package 'fasta3' in '../fasta3_36.3.8i.14-Nov-2020-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../fasta3_36.3.8i.14-Nov-2020-4_amd64.buildinfo dpkg-genchanges --build=binary -O../fasta3_36.3.8i.14-Nov-2020-4_amd64.changes @@ -2086,12 +2122,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3276862/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3276862/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1317710 and its subdirectories -I: Current time: Wed Sep 24 01:49:31 -12 2025 -I: pbuilder-time-stamp: 1758721771 +I: removing directory /srv/workspace/pbuilder/3276862 and its subdirectories +I: Current time: Wed Oct 28 10:20:05 +14 2026 +I: pbuilder-time-stamp: 1793132405