Diff of the two buildlogs: -- --- b1/build.log 2025-01-21 07:21:45.697400986 +0000 +++ b2/build.log 2025-01-21 07:24:03.387238558 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jan 20 19:19:34 -12 2025 -I: pbuilder-time-stamp: 1737443974 +I: Current time: Tue Feb 24 03:44:48 +14 2026 +I: pbuilder-time-stamp: 1771854288 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: applying adjust-scripts I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3156108/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3524965/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 Feb 23 13:44 /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/3524965/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3524965/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='7377492565234f1088b9e8f200556e62' - 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='3156108' - PS1='# ' - PS2='> ' + INVOCATION_ID=850965b79b3e4839933cfa08ec311c4b + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=3524965 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.wd6j35OO/pbuilderrc_Nvze --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wd6j35OO/b1 --logfile b1/build.log fasta3_36.3.8i.14-Nov-2020-3.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.wd6j35OO/pbuilderrc_uwAm --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wd6j35OO/b2 --logfile b2/build.log fasta3_36.3.8i.14-Nov-2020-3.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3156108/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3524965/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -140,7 +172,7 @@ Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libsimde-dev all 0.8.2-2 [467 kB] -Fetched 20.4 MB in 0s (138 MB/s) +Fetched 20.4 MB in 0s (80.0 MB/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 ... 19970 files and directories currently installed.) @@ -279,7 +311,11 @@ 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-2020-3_source.changes +I: user script /srv/workspace/pbuilder/3524965/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3524965/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-2020-3_source.changes dpkg-buildpackage: info: source package fasta3 dpkg-buildpackage: info: source version 36.3.8i.14-Nov-2020-3 dpkg-buildpackage: info: source distribution unstable @@ -326,8 +362,6 @@ 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 -mbranch-protection=standard -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 -DLOCAL_SCORE -c scaleswn.c -o scale_se.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 -mbranch-protection=standard -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 karlin.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 -mbranch-protection=standard -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 dropnfa.c -o drop_nfa.o -cc -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 -mbranch-protection=standard -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o wm_align.o wm_align.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 -mbranch-protection=standard -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 -DFASTA -c cal_cons2.c -o calcons_fa.o compacc2e.c: In function 'save_best': compacc2e.c:2569:87: warning: format '%lld' expects argument of type 'long long int', but argument 19 has type 'off_t' {aka 'long int'} [-Wformat=] 2569 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", @@ -352,10 +386,62 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | off_t {aka long int} +cc -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 -mbranch-protection=standard -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o wm_align.o wm_align.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 -mbranch-protection=standard -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 -DFASTA -c cal_cons2.c -o calcons_fa.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 -mbranch-protection=standard -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 nmgetlib.c -o lgetlib.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 -mbranch-protection=standard -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 mmgetaa.c -o lgetaa_m.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 -mbranch-protection=standard -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 c_dispn.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 -mbranch-protection=standard -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 ncbl2_mlib.c -o ncbl2_mlib.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 -mbranch-protection=standard -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 lib_sel.c +mmgetaa.c: In function 'load_mmap': +mmgetaa.c:167:63: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'fseek_t' {aka 'long int'} [-Wformat=] + 167 | 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:205:41: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '__off64_t' {aka 'long int'} [-Wformat=] + 205 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", + | ~~~^ + | | + | long long int + | %ld + 206 | bname,statbuf.st_size,f_size); + | ~~~~~~~~~~~~~~~ + | | + | __off64_t {aka long int} +mmgetaa.c:205:66: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'fseek_t' {aka 'long int'} [-Wformat=] + 205 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", + | ~~~^ + | | + | long long int + | %ld + 206 | bname,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 -mbranch-protection=standard -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 url_subs.c +mmgetaa.c:296:59: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '__off64_t' {aka 'long int'} [-Wformat=] + 296 | fprintf(stderr,"*** ERROR [%s:%d] %s file size (%lld) and expected size (%lld) don't match\n", + | ~~~^ + | | + | long long int + | %ld + 297 | __FILE__, __LINE__, sname,statbuf.st_size,f_size); + | ~~~~~~~~~~~~~~~ + | | + | __off64_t {aka long int} +mmgetaa.c:296:84: warning: format '%lld' expects argument of type 'long long int', but argument 7 has type 'fseek_t' {aka 'long int'} [-Wformat=] + 296 | fprintf(stderr,"*** ERROR [%s:%d] %s file size (%lld) and expected size (%lld) don't match\n", + | ~~~^ + | | + | long long int + | %ld + 297 | __FILE__, __LINE__, sname,statbuf.st_size,f_size); + | ~~~~~~ + | | + | fseek_t {aka long int} +mmgetaa.c: In function 'check_mmap': 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); @@ -370,6 +456,16 @@ 696 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function 'aranlib': +mmgetaa.c:1077:31: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'MM_OFF' {aka 'long int'} [-Wformat=] + 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", + | ~~~^ + | | + | long long int + | %ld + 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], + | ~~~~~~~~~~~~~~~~~~ + | | + | MM_OFF {aka long int} 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -383,10 +479,31 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mmgetaa.c:1077:37: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'MM_OFF' {aka 'long int'} [-Wformat=] + 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", + | ~~~^ + | | + | long long int + | %ld + 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], + | ~~~~~~~~~~~~~~~~~~ + | | + | MM_OFF {aka long int} 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mmgetaa.c:1077:43: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'MM_OFF' {aka 'long int'} [-Wformat=] + 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", + | ~~~^ + | | + | long long int + | %ld + 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], + 1079 | m_fd->d_pos_arr[i+1]-m_fd->s_pos_arr[i]); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | + | MM_OFF {aka long int} nmgetlib.c: In function 'lgetlib': 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); @@ -497,6 +614,17 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c: In function 'ncbl2_getliba': +ncbl2_mlib.c:1105:78: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'fseek_t' {aka 'long int'} [-Wformat=] + 1105 | fprintf(stderr,"*** ERROR [%s:%d] - could not read sequence record: %lld %ld != %ld\n", + | ~~~^ + | | + | long long int + | %ld + 1106 | __FILE__,__LINE__, *libpos,tmp,seq_len); + | ~~~~~~~ + | | + | fseek_t {aka long int} 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); @@ -507,6 +635,12 @@ nmgetlib.c:1575:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1575 | fgets(&lm_fd->lline[strlen(lm_fd->lline)-MAX_STR/2],MAX_STR/2,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +ncbl2_mlib.c:1150:68: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'fseek_t' {aka 'long int'} [-Wformat=] + 1150 | error: fprintf(stderr,"*** ERROR [%s:%d] - error reading %s at %lld\n",__FILE__,__LINE__,libstr,*libpos); + | ~~~^ ~~~~~~~ + | | | + | long long int fseek_t {aka long int} + | %ld nmgetlib.c:1595:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1595 | fread((char *)seqp,(size_t)r_block,(size_t)1,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -523,105 +657,6 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mmgetaa.c: In function 'load_mmap': -mmgetaa.c:167:63: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'fseek_t' {aka 'long int'} [-Wformat=] - 167 | 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:205:41: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '__off64_t' {aka 'long int'} [-Wformat=] - 205 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", - | ~~~^ - | | - | long long int - | %ld - 206 | bname,statbuf.st_size,f_size); - | ~~~~~~~~~~~~~~~ - | | - | __off64_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 -mbranch-protection=standard -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 lib_sel.c -mmgetaa.c:205:66: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'fseek_t' {aka 'long int'} [-Wformat=] - 205 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", - | ~~~^ - | | - | long long int - | %ld - 206 | bname,statbuf.st_size,f_size); - | ~~~~~~ - | | - | fseek_t {aka long int} -mmgetaa.c:296:59: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '__off64_t' {aka 'long int'} [-Wformat=] - 296 | fprintf(stderr,"*** ERROR [%s:%d] %s file size (%lld) and expected size (%lld) don't match\n", - | ~~~^ - | | - | long long int - | %ld - 297 | __FILE__, __LINE__, sname,statbuf.st_size,f_size); - | ~~~~~~~~~~~~~~~ - | | - | __off64_t {aka long int} -mmgetaa.c:296:84: warning: format '%lld' expects argument of type 'long long int', but argument 7 has type 'fseek_t' {aka 'long int'} [-Wformat=] - 296 | fprintf(stderr,"*** ERROR [%s:%d] %s file size (%lld) and expected size (%lld) don't match\n", - | ~~~^ - | | - | long long int - | %ld - 297 | __FILE__, __LINE__, sname,statbuf.st_size,f_size); - | ~~~~~~ - | | - | fseek_t {aka long int} -mmgetaa.c: In function 'check_mmap': -mmgetaa.c:1077:31: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'MM_OFF' {aka 'long int'} [-Wformat=] - 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", - | ~~~^ - | | - | long long int - | %ld - 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], - | ~~~~~~~~~~~~~~~~~~ - | | - | MM_OFF {aka long int} -mmgetaa.c:1077:37: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'MM_OFF' {aka 'long int'} [-Wformat=] - 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", - | ~~~^ - | | - | long long int - | %ld - 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], - | ~~~~~~~~~~~~~~~~~~ - | | - | MM_OFF {aka long int} -mmgetaa.c:1077:43: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'MM_OFF' {aka 'long int'} [-Wformat=] - 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", - | ~~~^ - | | - | long long int - | %ld - 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], - 1079 | m_fd->d_pos_arr[i+1]-m_fd->s_pos_arr[i]); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | MM_OFF {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 -mbranch-protection=standard -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 url_subs.c -cc -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 -mbranch-protection=standard -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mrandom.o mrandom.c -ncbl2_mlib.c: In function 'ncbl2_getliba': -ncbl2_mlib.c:1105:78: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'fseek_t' {aka 'long int'} [-Wformat=] - 1105 | fprintf(stderr,"*** ERROR [%s:%d] - could not read sequence record: %lld %ld != %ld\n", - | ~~~^ - | | - | long long int - | %ld - 1106 | __FILE__,__LINE__, *libpos,tmp,seq_len); - | ~~~~~~~ - | | - | fseek_t {aka long int} -ncbl2_mlib.c:1150:68: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'fseek_t' {aka 'long int'} [-Wformat=] - 1150 | error: fprintf(stderr,"*** ERROR [%s:%d] - error reading %s at %lld\n",__FILE__,__LINE__,libstr,*libpos); - | ~~~^ ~~~~~~~ - | | | - | long long int fseek_t {aka long int} - | %ld ncbl2_mlib.c: In function 'ncbl2_getlibn': ncbl2_mlib.c:1434:76: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'fseek_t' {aka 'long int'} [-Wformat=] 1434 | "*** ERROR [%s:%d] - could not read sequence record: %s %lld %ld != %ld: %d\n", @@ -649,7 +684,7 @@ | | | | long long int fseek_t {aka long int} | %ld -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 -mbranch-protection=standard -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 -DSSEARCH initfa.c -o init_sw_sse.o +cc -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 -mbranch-protection=standard -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mrandom.o mrandom.c ncbl2_mlib.c: In function 'load_ncbl2': 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); @@ -660,7 +695,6 @@ 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 -mbranch-protection=standard -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 dropgsw2.c -o dropgsw2_sse.o 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); @@ -696,6 +730,8 @@ 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 -mbranch-protection=standard -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 -DSSEARCH initfa.c -o init_sw_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 -mbranch-protection=standard -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 dropgsw2.c -o dropgsw2_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 -mbranch-protection=standard -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 smith_waterman_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 -mbranch-protection=standard -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 wm_align.c -o lwm_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 -mbranch-protection=standard -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 -DSSEARCH -c cal_cons2.c -o calcons_sw.o @@ -790,7 +826,6 @@ map_db.c:149:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 149 | fgets(lname,sizeof(lname),stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 map_db.c: In function 'gbf_get_ent': map_db.c:512:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 512 | fgets(lline,MAXLINE,libf); @@ -799,12 +834,11 @@ map_db.c:524:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 524 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/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/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 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); | ^ @@ -822,6 +856,13 @@ 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: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, | ^ @@ -829,6 +870,7 @@ 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' +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 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] @@ -838,7 +880,7 @@ 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 +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); | ^ @@ -856,13 +898,14 @@ 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: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, | ^ @@ -896,16 +939,6 @@ 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: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, - | ^ -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: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, | ^ @@ -922,6 +955,9 @@ 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) | ^ @@ -959,6 +995,7 @@ 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); | ^ @@ -1016,14 +1053,13 @@ 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: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 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, | ^ @@ -1097,14 +1133,13 @@ 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: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 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, | ^ @@ -1138,13 +1173,14 @@ 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: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, | ^ @@ -1453,21 +1489,21 @@ 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 Tue Jan 21 07:20:53 2025 on codethink04-arm64 -Linux codethink04-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux +STARTING FASTA36 Mon Feb 23 13:46:10 2026 on i-capture-the-hostname +Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux -starting prss36(ssearch/fastx) Tue Jan 21 07:20:53 2025 +starting prss36(ssearch/fastx) Mon Feb 23 13:46:10 2026 done -starting lalign36 Tue Jan 21 07:20:53 2025 -FINISHED Tue Jan 21 07:21:11 2025 +starting lalign36 Mon Feb 23 13:46:10 2026 +FINISHED Mon Feb 23 13:46:26 2026 -STARTING FASTA36 Tue Jan 21 07:21:11 2025 on codethink04-arm64 -Linux codethink04-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux +STARTING FASTA36 Mon Feb 23 13:46:26 2026 on i-capture-the-hostname +Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux -starting prss36(ssearch/fastx) Tue Jan 21 07:21:11 2025 +starting prss36(ssearch/fastx) Mon Feb 23 13:46:26 2026 done -starting lalign36 Tue Jan 21 07:21:12 2025 -FINISHED Tue Jan 21 07:21:29 2025 +starting lalign36 Mon Feb 23 13:46:26 2026 +FINISHED Mon Feb 23 13:46:43 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 @@ -1479,29 +1515,29 @@ Library: ../seq/prot_test.lseg 2267 residues in 12 sequences -Statistics: (shuffled [424]) MLE statistics: Lambda= 0.1407; K=0.00259 - statistics sampled from 4 (4) to 424 sequences +Statistics: (shuffled [431]) MLE statistics: Lambda= 0.1661; K=0.005336 + statistics sampled from 4 (4) to 430 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: 0.000 + Scan time: 0.020 The best scores are: opt bits E(12) -sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 262.4 5.7e-74 -sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 58.4 1.5e-12 -sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 20.6 0.23 -sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 19.0 1.6 -sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 17.6 1.7 -sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 16.6 2.6 -sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 16.4 2.8 -sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.4 4.1 -sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.7 4.2 -sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.6 4.2 -sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 17.8 5 -sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 14.9 6.2 +sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 307.3 1.8e-87 +sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 66.5 5.8e-15 +sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 21.9 0.096 +sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 20.0 0.86 +sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 18.3 1.1 +sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 17.1 1.9 +sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 16.8 2.1 +sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.8 3.1 +sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 18.5 3.3 +sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.9 3.5 +sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.9 3.8 +sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 15.2 5.6 >>sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 O (218 aa) - initn: 1242 init1: 1242 opt: 1242 Z-score: 1379.8 bits: 262.4 E(12): 5.7e-74 + initn: 1242 init1: 1242 opt: 1242 Z-score: 1622.1 bits: 307.3 E(12): 1.8e-87 Smith-Waterman score: 1242; 78.0% identity (95.4% similar) in 218 aa overlap (1-218:1-218) 10 20 30 40 50 60 @@ -1529,7 +1565,7 @@ 190 200 210 >>sp|P00502|GSTA1_RAT Glutathione S-transferase alpha-1 (222 aa) - initn: 204 init1: 73 opt: 237 Z-score: 277.0 bits: 58.4 E(12): 1.5e-12 + initn: 204 init1: 73 opt: 237 Z-score: 320.5 bits: 66.5 E(12): 5.8e-15 Smith-Waterman score: 237; 27.4% identity (57.0% similar) in 223 aa overlap (4-218:6-218) 10 20 30 40 50 @@ -1557,7 +1593,7 @@ 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: 76.4 bits: 20.6 E(12): 0.23 + initn: 40 init1: 40 opt: 51 Z-score: 83.1 bits: 21.9 E(12): 0.096 Smith-Waterman score: 51; 25.6% identity (69.2% similar) in 39 aa overlap (177-214:36-73) 150 160 170 180 190 200 @@ -1573,7 +1609,7 @@ 70 80 90 100 110 120 >>sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinase ca (351 aa) - initn: 43 init1: 43 opt: 43 Z-score: 60.5 bits: 19.0 E(12): 1.6 + initn: 43 init1: 43 opt: 43 Z-score: 65.7 bits: 20.0 E(12): 0.86 Smith-Waterman score: 54; 23.6% identity (47.2% similar) in 72 aa overlap (137-206:229-300) 110 120 130 140 150 160 @@ -1592,7 +1628,7 @@ 320 330 340 350 >>sp|P14960|RBS_GUITH Ribulose bisphosphate carboxylase (139 aa) - initn: 56 init1: 36 opt: 36 Z-score: 60.1 bits: 17.6 E(12): 1.7 + initn: 56 init1: 36 opt: 36 Z-score: 63.9 bits: 18.3 E(12): 1.1 Smith-Waterman score: 36; 57.1% identity (85.7% similar) in 7 aa overlap (7-13:47-53) 10 20 30 @@ -1608,7 +1644,7 @@ 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: 56.6 bits: 16.6 E(12): 2.6 + initn: 31 init1: 31 opt: 31 Z-score: 59.4 bits: 17.1 E(12): 1.9 Smith-Waterman score: 33; 36.0% identity (54.0% similar) in 50 aa overlap (150-190:16-64) 120 130 140 150 160 170 @@ -1624,7 +1660,7 @@ 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: 55.7 bits: 16.4 E(12): 2.8 + initn: 30 init1: 30 opt: 30 Z-score: 58.3 bits: 16.8 E(12): 2.1 Smith-Waterman score: 36; 26.5% identity (54.4% similar) in 68 aa overlap (129-193:28-88) 100 110 120 130 140 150 @@ -1643,7 +1679,7 @@ sp|P10 SNK >>sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle OS=H (160 aa) - initn: 30 init1: 30 opt: 30 Z-score: 52.4 bits: 16.4 E(12): 4.1 + initn: 30 init1: 30 opt: 30 Z-score: 55.0 bits: 16.8 E(12): 3.1 Smith-Waterman score: 41; 25.9% identity (63.0% similar) in 54 aa overlap (44-92:13-62) 20 30 40 50 60 70 @@ -1658,24 +1694,24 @@ 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: 52.1 bits: 14.7 E(12): 4.2 -Smith-Waterman score: 25; 50.0% identity (100.0% similar) in 4 aa overlap (171-174:15-18) +>>sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A viru (567 aa) + initn: 37 init1: 37 opt: 37 Z-score: 54.2 bits: 18.5 E(12): 3.3 +Smith-Waterman score: 50; 28.2% identity (64.1% similar) in 39 aa overlap (74-111:399-437) - 150 160 170 180 190 200 -sp|P10 FLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKS - .:.: -sp|P00 AYVINDSCIACGACKPECPVNIQQGSIYAIDADSCIDCGSCASV - 10 20 30 40 + 50 60 70 80 90 100 +sp|P10 SQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARK-HHLDGETEEERIRADIVEN + : ... .: :... : : . : . .:. +sp|P03 GFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEK + 370 380 390 400 410 420 - 210 -sp|P10 SRYIATPIFSKMAHWSNK - -sp|P00 CPVGAPNPED - 50 + 110 120 130 140 150 160 +sp|P10 QVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYD + : ::...: +sp|P03 YVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYH + 430 440 450 460 470 480 >>sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A31 O (95 aa) - initn: 26 init1: 26 opt: 26 Z-score: 52.1 bits: 15.6 E(12): 4.2 + initn: 26 init1: 26 opt: 26 Z-score: 53.9 bits: 15.9 E(12): 3.5 Smith-Waterman score: 30; 54.5% identity (63.6% similar) in 11 aa overlap (115-125:86-94) 90 100 110 120 130 140 @@ -1687,24 +1723,24 @@ 150 160 170 180 190 200 sp|P10 RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYI ->>sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A viru (567 aa) - initn: 37 init1: 37 opt: 37 Z-score: 50.2 bits: 17.8 E(12): 5 -Smith-Waterman score: 50; 28.2% identity (64.1% similar) in 39 aa overlap (74-111:399-437) +>>sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococcus a (54 aa) + initn: 22 init1: 22 opt: 22 Z-score: 53.1 bits: 14.9 E(12): 3.8 +Smith-Waterman score: 25; 50.0% identity (100.0% similar) in 4 aa overlap (171-174:15-18) - 50 60 70 80 90 100 -sp|P10 SQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARK-HHLDGETEEERIRADIVEN - : ... .: :... : : . : . .:. -sp|P03 GFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEK - 370 380 390 400 410 420 + 150 160 170 180 190 200 +sp|P10 FLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKS + .:.: +sp|P00 AYVINDSCIACGACKPECPVNIQQGSIYAIDADSCIDCGSCASV + 10 20 30 40 - 110 120 130 140 150 160 -sp|P10 QVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYD - : ::...: -sp|P03 YVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYH - 430 440 450 460 470 480 + 210 +sp|P10 SRYIATPIFSKMAHWSNK + +sp|P00 CPVGAPNPED + 50 >>sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Homo s (106 aa) - initn: 23 init1: 23 opt: 23 Z-score: 47.9 bits: 14.9 E(12): 6.2 + initn: 23 init1: 23 opt: 23 Z-score: 49.2 bits: 15.2 E(12): 5.6 Smith-Waterman score: 35; 18.3% identity (53.5% similar) in 71 aa overlap (58-124:12-82) 30 40 50 60 70 80 @@ -1730,8 +1766,8 @@ 218 residues in 1 query sequences 2267 residues in 12 library sequences Tcomplib [36.3.8i Nov, 2022] (12 proc in memory [0G]) - start: Tue Jan 21 07:21:29 2025 done: Tue Jan 21 07:21:29 2025 - Total Scan time: 0.000 Total Display time: 0.010 + start: Mon Feb 23 13:46:43 2026 done: Mon Feb 23 13:46:43 2026 + Total Scan time: 0.020 Total Display time: 0.010 Function used was FASTA [36.3.8i Nov, 2022] rm -rf test/results/test* @@ -1767,9 +1803,9 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src +dpkg-deb: building package 'fasta3-dbgsym' in '../fasta3-dbgsym_36.3.8i.14-Nov-2020-3_arm64.deb'. dpkg-deb: building package 'fasta3' in '../fasta3_36.3.8i.14-Nov-2020-3_arm64.deb'. dpkg-deb: building package 'fasta3-doc' in '../fasta3-doc_36.3.8i.14-Nov-2020-3_all.deb'. -dpkg-deb: building package 'fasta3-dbgsym' in '../fasta3-dbgsym_36.3.8i.14-Nov-2020-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../fasta3_36.3.8i.14-Nov-2020-3_arm64.buildinfo dpkg-genchanges --build=binary -O../fasta3_36.3.8i.14-Nov-2020-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1777,12 +1813,14 @@ 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/3524965/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3524965/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/3156108 and its subdirectories -I: Current time: Mon Jan 20 19:21:44 -12 2025 -I: pbuilder-time-stamp: 1737444104 +I: removing directory /srv/workspace/pbuilder/3524965 and its subdirectories +I: Current time: Tue Feb 24 03:47:02 +14 2026 +I: pbuilder-time-stamp: 1771854422