Diff of the two buildlogs: -- --- b1/build.log 2025-09-08 19:55:47.110100789 +0000 +++ b2/build.log 2025-09-08 19:56:37.506166221 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Sep 8 07:53:42 -12 2025 -I: pbuilder-time-stamp: 1757361222 +I: Current time: Mon Oct 12 16:18:48 +14 2026 +I: pbuilder-time-stamp: 1791771528 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -33,53 +33,85 @@ dpkg-source: info: applying increase_max_pid.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2895338/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3864704/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 12 02:18 /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/3864704/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3864704/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='forky' - 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=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='4c75a084946045e59578b853cb7ca4a6' - 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='2895338' - PS1='# ' - PS2='> ' + INVOCATION_ID=be2ab65656f64cf0a4e48f4ee386ce1e + 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=3864704 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.hcrqcaAJ/pbuilderrc_jwGU --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hcrqcaAJ/b1 --logfile b1/build.log t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.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.hcrqcaAJ/pbuilderrc_1CXN --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hcrqcaAJ/b2 --logfile b2/build.log t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.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 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) 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/2895338/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3864704/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -144,7 +176,7 @@ Get: 27 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] -Fetched 11.2 MB in 4s (2890 kB/s) +Fetched 11.2 MB in 1s (13.1 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 ... 19898 files and directories currently installed.) @@ -275,7 +307,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/ && 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 > ../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/3864704/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/3864704/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/ && 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 > ../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_source.changes dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -302,122 +338,128 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_auto_build -- USER_BIN=../bin/ FCC="gfortran -g -O2 -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection" 'CC=$(CXX)' all - cd t_coffee_source && make -j40 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection" CC=\$\(CXX\) all + cd t_coffee_source && make -j42 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection" CC=\$\(CXX\) all make[2]: Entering directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/t_coffee_source' CC dev_lib/dev1.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dev_lib/dev1.deps -c -o dev_lib/dev1.o dev_lib/dev1.c CC dp_lib/CUSTOM_evaluate_for_struc.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dev_lib/dev1.deps -c -o dev_lib/dev1.o dev_lib/dev1.c CC dp_lib/evaluate.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c CC dp_lib/evaluate_dirichlet.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c CC dp_lib/evaluate_for_domain.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c CC dp_lib/evaluate_for_struc.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c CC dp_lib/fsa_dp.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o dp_lib/fsa_dp.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c CC dp_lib/pavie_dp.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o dp_lib/fsa_dp.c CC dp_lib/showpair.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/showpair.deps -c -o dp_lib/showpair.o dp_lib/showpair.c CC dp_lib/util_domain_dp.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o dp_lib/util_domain_dp.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_domain_dp_drivers.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp_drivers.deps -c -o dp_lib/util_domain_dp_drivers.o dp_lib/util_domain_dp_drivers.c CC dp_lib/util_dp_cdna_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_cdna_fasta_nw.deps -c -o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_cdna_fasta_nw.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_clean_maln.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_clean_maln.deps -c -o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_clean_maln.c CC dp_lib/util_dp_drivers.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_clean_maln.deps -c -o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_clean_maln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_drivers.deps -c -o dp_lib/util_dp_drivers.o dp_lib/util_dp_drivers.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_est.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_est.deps -c -o dp_lib/util_dp_est.o dp_lib/util_dp_est.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/util_dp_fasta_nw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c CC dp_lib/util_dp_fasta_sw.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c CC dp_lib/util_dp_generic_fasta_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c CC dp_lib/util_dp_gotoh_nw.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_nw.deps -c -o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_nw.c CC dp_lib/util_dp_gotoh_sw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC dp_lib/util_dp_mm_nw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC dp_lib/util_dp_mm_nw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c CC dp_lib/util_dp_sim.c CC dp_lib/util_dp_ssec_pwaln.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_sim.deps -c -o dp_lib/util_dp_sim.o dp_lib/util_dp_sim.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_ssec_pwaln.deps -c -o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_ssec_pwaln.c CC dp_lib/util_dp_suboptimal_nw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c CC dp_lib/util_graph_maln.c - CC fastal/diagonal.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c + CC fastal/diagonal.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c CC fastal/fastal.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC fastal/fastal_opt_parsing.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal_opt_parsing.deps -c -o fastal/fastal_opt_parsing.o fastal/fastal_opt_parsing.c CC fastal/iteration.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC fastal/parttree.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.c CC fastal/scoring.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/scoring.deps -c -o fastal/scoring.o fastal/scoring.c CC fastal/tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/tree.deps -c -o fastal/tree.o fastal/tree.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC io_lib/io_func.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/io_func.deps -c -o io_lib/io_func.o io_lib/io_func.c CC io_lib/pb_util_read_seq_util.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c CC io_lib/pb_util_read_sequence.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC io_lib/tree_util.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/tree_util.deps -c -o io_lib/tree_util.o io_lib/tree_util.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC km_coffee/Stack.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c CC km_coffee/Vector.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c CC km_coffee/classes.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c CC km_coffee/km_coffee.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_coffee.deps -c -o km_coffee/km_coffee.o km_coffee/km_coffee.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_coffee.deps -c -o km_coffee/km_coffee.o km_coffee/km_coffee.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC km_coffee/km_util.c + CC km_coffee/kmeans.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_util.deps -c -o km_coffee/km_util.o km_coffee/km_util.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/kmeans.deps -c -o km_coffee/kmeans.o km_coffee/kmeans.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ @@ -434,6 +476,16 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from io_lib/pb_util_read_sequence.c:35: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from io_lib/io_func.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ io_lib/pb_util_read_seq_util.c: In function 'void* ckalloc(size_t)': io_lib/pb_util_read_seq_util.c:68:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 68 | register void *ret; @@ -458,6 +510,13 @@ io_lib/pb_util_read_seq_util.c:356:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 356 | register int i; | ^ +io_lib/pb_util_read_sequence.c: In function 'void fill_chartab()': +io_lib/pb_util_read_sequence.c:79:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 79 | register int i; + | ^ +io_lib/pb_util_read_sequence.c:80:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 80 | register int c; + | ^ io_lib/pb_util_read_seq_util.c: In function 'void getstr(char*, char*)': io_lib/pb_util_read_seq_util.c:269:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | fgets(outstr, 100, stdin); @@ -470,71 +529,6 @@ io_lib/pb_util_read_seq_util.c:305:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from io_lib/io_func.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from io_lib/pb_util_read_sequence.c:35: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_est.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_clean_maln.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/pavie_dp.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/evaluate_for_domain.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -fastal/diagonal.c: In function 'int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)': -fastal/diagonal.c:434:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 434 | system(blast_command); - | ~~~~~~^~~~~~~~~~~~~~~ -fastal/diagonal.c:439:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 439 | fgets(line, 300, diag_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/diagonal.c:440:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 440 | fgets(line, 300, diag_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/diagonal.c:441:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 441 | fgets(line, 300, diag_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/evaluate_for_struc.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/evaluate_dirichlet.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -io_lib/pb_util_read_sequence.c: In function 'void fill_chartab()': -io_lib/pb_util_read_sequence.c:79:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 79 | register int i; - | ^ -io_lib/pb_util_read_sequence.c:80:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 80 | register int c; - | ^ -In file included from ./io_lib_header.h:33, - from dp_lib/fsa_dp.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ io_lib/pb_util_read_sequence.c: In function 'void get_clustal_seq(char*, char*, int*, char*, int)': io_lib/pb_util_read_sequence.c:144:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 144 | fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ @@ -565,20 +559,23 @@ io_lib/pb_util_read_sequence.c:280:46: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 280 | fgets(line,MAXLINE+1,fin); | ~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_sim.c:32: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ +fastal/diagonal.c: In function 'int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)': +fastal/diagonal.c:434:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 434 | system(blast_command); + | ~~~~~~^~~~~~~~~~~~~~~ +fastal/diagonal.c:439:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 439 | fgets(line, 300, diag_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/diagonal.c:440:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 440 | fgets(line, 300, diag_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/diagonal.c:441:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 441 | fgets(line, 300, diag_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~ io_lib/io_func.c: In function 'int output_raw_score(Alignment*, Alignment*, char*)': io_lib/io_func.c:1235:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null] 1235 | if (!A)return NULL; | ^~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_cdna_fasta_nw.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ io_lib/io_func.c: In function 'int aln2compressed_ps(Alignment*, char*)': io_lib/io_func.c:2076:1: warning: no return statement in function returning non-void [-Wreturn-type] 2076 | } @@ -591,17 +588,31 @@ io_lib/io_func.c:971:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 971 | fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC t_coffee_lib/t_coffee.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF t_coffee_lib/t_coffee.deps -c -o t_coffee_lib/t_coffee.o t_coffee_lib/t_coffee.c In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_generic_fasta_nw.c:34: + from dp_lib/evaluate_for_struc.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -dp_lib/pavie_dp.c: In function 'double** pavie_seq2pavie_aln(Sequence*, char*, char*)': -dp_lib/pavie_dp.c:127:18: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 127 | fscanf (fp, "%s\n",mat_list[nch++]); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, - from dp_lib/util_domain_dp.c:33: + from dev_lib/dev1.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/pavie_dp.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/evaluate_dirichlet.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_clean_maln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ @@ -611,23 +622,97 @@ 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, + from dp_lib/evaluate_for_domain.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/fsa_dp.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_domain_dp.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_fasta_sw.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/CUSTOM_evaluate_for_struc.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_est.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_fasta_nw.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/showpair.c:32: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_cdna_fasta_nw.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_sim.c:32: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/evaluate.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_gotoh_sw.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_drivers.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_gotoh_nw.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, from dp_lib/util_graph_maln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': -dp_lib/pavie_dp.c:1079:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1079 | system (command); - | ~~~~~~~~^~~~~~~~~ -dp_lib/pavie_dp.c:1081:14: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1081 | system (command); - | ~~~~~~~^~~~~~~~~ -dp_lib/pavie_dp.c: In function 'Alignment* pavie_seq2pavie_msa(Sequence*, char*, char*)': -dp_lib/pavie_dp.c:1365:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1365 | fscanf (fp, "%s", mat); - | ~~~~~~~^~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from fastal/scoring.c:37: + from dp_lib/util_dp_suboptimal_nw.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_mm_nw.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_generic_fasta_nw.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from fastal/parttree.c:36: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ @@ -636,23 +721,52 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from fastal/fastal.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from fastal/iteration.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from fastal/scoring.c:37: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +km_coffee/km_util.c: In function 'char* my_make_temp_dir(char*, char*)': +km_coffee/km_util.c:96:69: warning: format '%s' expects a matching 'char*' argument [-Wformat=] + 96 | fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); + | ~^ + | | + | char* + CC util_lib/aln_compare.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_compare.deps -c -o util_lib/aln_compare.o util_lib/aln_compare.c +dev_lib/dev1.c: In function 'void aln2hitMat(Alignment*, char*)': +dev_lib/dev1.c:89:26: warning: too many arguments for format [-Wformat-extra-args] + 89 | fprintf (stdout, "Process positions\n", i); + | ^~~~~~~~~~~~~~~~~~~~~ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_ssec_pwaln.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +dp_lib/util_dp_fasta_nw.c: In function 'int* makepointtable(int*, int*, int)': +dp_lib/util_dp_fasta_nw.c:157:17: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 157 | register int *p; + | ^ +In file included from ./io_lib_header.h:33, + from km_coffee/km_coffee.c:43: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ dp_lib/util_dp_sim.c: In function 'int addnode(int, int, int, int, int, int, int)': dp_lib/util_dp_sim.c:173:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 173 | register int d; | ^ -dp_lib/evaluate_dirichlet.c: In function 'Mixture* read_dirichlet(char*)': -dp_lib/evaluate_dirichlet.c:317:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 317 | fscanf(fp, "%f\n", &f); - | ~~~~~~^~~~~~~~~~~~~~~~ -dp_lib/evaluate_dirichlet.c:319:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 319 | fscanf(fp, "%f", &f); - | ~~~~~~^~~~~~~~~~~~~~ -dp_lib/evaluate_dirichlet.c:323:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 323 | fscanf(fp, "%f", &f); - | ~~~~~~^~~~~~~~~~~~~~ -dp_lib/evaluate_dirichlet.c:326:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 326 | fscanf(fp, "\n"); - | ~~~~~~^~~~~~~~~~ dp_lib/util_dp_sim.c: In function 'int sim_pair_wise_lalign(Alignment*, int*, int**, Constraint_list*)': dp_lib/util_dp_sim.c:248:20: warning: empty parentheses were disambiguated as a function declaration [-Wvexing-parse] 248 | vertexptr findmax(); /* return the largest score node */ @@ -662,16 +776,6 @@ | ^~ | -- dp_lib/util_dp_sim.c:248:20: note: or replace parentheses with braces to value-initialize a variable -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_fasta_sw.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_suboptimal_nw.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ dp_lib/util_dp_sim.c: In function 'int big_pass(int*, int*, int, int, int, int)': dp_lib/util_dp_sim.c:481:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 481 | { register int i, j; /* row and column indices */ @@ -715,6 +819,11 @@ dp_lib/util_dp_sim.c:489:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 489 | register int pi, pj; /* end-point associated with p */ | ^~ +In file included from ./io_lib_header.h:33, + from io_lib/tree_util.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ dp_lib/util_dp_sim.c: In function 'int locate(int*, int*, int)': dp_lib/util_dp_sim.c:562:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 562 | { register int i, j; /* row and column indices */ @@ -766,16 +875,6 @@ | ^~ | -- dp_lib/util_dp_sim.c:572:16: note: or replace parentheses with braces to value-initialize a variable -In file included from ./io_lib_header.h:33, - from dev_lib/dev1.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/showpair.c:32: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ dp_lib/util_dp_sim.c: In function 'int small_pass(int*, int*, int, int)': dp_lib/util_dp_sim.c:786:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 786 | { register int i, j; /* row and column indices */ @@ -819,8 +918,6 @@ dp_lib/util_dp_sim.c:794:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 794 | register int pi, pj; /* end-point associated with p */ | ^~ - CC km_coffee/km_util.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_util.deps -c -o km_coffee/km_util.o km_coffee/km_util.c dp_lib/util_dp_sim.c: In function 'SIM_NODE* findmax()': dp_lib/util_dp_sim.c:864:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 864 | register int i, j; @@ -848,43 +945,121 @@ dp_lib/util_dp_sim.c:912:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_ssec_pwaln.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ dp_lib/util_dp_sim.c:912:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_mm_nw.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_fasta_nw.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_drivers.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/evaluate.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -dev_lib/dev1.c: In function 'void aln2hitMat(Alignment*, char*)': -dev_lib/dev1.c:89:26: warning: too many arguments for format [-Wformat-extra-args] - 89 | fprintf (stdout, "Process positions\n", i); +fastal/parttree.c: In function 'void makepointtable_fast(int*, int, int, int)': +fastal/parttree.c:757:23: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 757 | register int *p; + | ^ +dp_lib/util_dp_drivers.c: In function 'Constraint_list* sap_pair(char*, char*, Constraint_list*)': +dp_lib/util_dp_drivers.c:2051:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2051 | register int a; + | ^ +dp_lib/evaluate_dirichlet.c: In function 'Mixture* read_dirichlet(char*)': +dp_lib/evaluate_dirichlet.c:317:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 317 | fscanf(fp, "%f\n", &f); + | ~~~~~~^~~~~~~~~~~~~~~~ +dp_lib/evaluate_dirichlet.c:319:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 319 | fscanf(fp, "%f", &f); + | ~~~~~~^~~~~~~~~~~~~~ +dp_lib/evaluate_dirichlet.c:323:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 323 | fscanf(fp, "%f", &f); + | ~~~~~~^~~~~~~~~~~~~~ +dp_lib/evaluate_dirichlet.c:326:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 326 | fscanf(fp, "\n"); + | ~~~~~~^~~~~~~~~~ +dp_lib/evaluate.c: In function 'Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)': +dp_lib/evaluate.c:3070:67: warning: format '%f' expects argument of type 'double', but argument 4 has type 'int' [-Wformat=] + 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); + | ~~~~^ ~~~ + | | | + | double int + | %3.2d +dp_lib/evaluate.c:3070:81: warning: format '%d' expects argument of type 'int', but argument 5 has type 'double' [-Wformat=] + 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); + | ~~^ ~~~~~~~ + | | | + | int double + | %3f +dp_lib/evaluate.c:3070:93: warning: format '%f' expects argument of type 'double', but argument 6 has type 'int' [-Wformat=] + 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); + | ~~~^ ~~~~~~~~ + | | | + | double int + | %.3d +dp_lib/evaluate.c:3070:109: warning: format '%d' expects argument of type 'int', but argument 7 has type 'double' [-Wformat=] + 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); + | ~~^ ~~~~~~ + | | | + | int double + | %3f +dp_lib/pavie_dp.c: In function 'double** pavie_seq2pavie_aln(Sequence*, char*, char*)': +dp_lib/pavie_dp.c:127:18: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 127 | fscanf (fp, "%s\n",mat_list[nch++]); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +dp_lib/util_dp_gotoh_sw.c: In function 'int gotoh_pair_wise_sw(Alignment*, int*, int**, Constraint_list*)': +dp_lib/util_dp_gotoh_sw.c:391:42: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 391 | fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +io_lib/tree_util.c: In function 'tnode* tree_scan(Alignment*, NT_node, char*, char*)': +io_lib/tree_util.c:836:26: warning: too many arguments for format [-Wformat-extra-args] + 836 | fprintf (stdout, "Process positions\n", i); | ^~~~~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_gotoh_sw.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ +fastal/iteration.c: In function 'void split_set(FILE*, Fastal_profile*, Fastal_profile*, char*, int, int*, char*)': +fastal/iteration.c:185:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 185 | fgets(line, LINE_LENGTH , alignment_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC util_lib/aln_convertion_util.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_convertion_util.deps -c -o util_lib/aln_convertion_util.o util_lib/aln_convertion_util.c +fastal/iteration.c: In function 'void iterate(Fastal_param*, void*, char*, char*, int)': +fastal/iteration.c:310:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 310 | fgets(line, LINE_LENGTH , alignment_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:435:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 435 | system(command); + | ~~~~~~^~~~~~~~~ +fastal/iteration.c: In function 'void write_iterated_aln(char*, char*, char*, char*, int*, int, char*, int*, int)': +fastal/iteration.c:501:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 501 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:504:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 504 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:535:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 535 | fgets(alnline, ALNLINE_LENGTH, old_aln_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c: In function 'void edit2seq_pattern(FILE*, char*, char*)': +fastal/iteration.c:563:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:565:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 565 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:567:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 567 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:569:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 569 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +io_lib/tree_util.c: In function 'Alignment* phylotrim(Alignment*, NT_node, char*, char*, char*)': +io_lib/tree_util.c:1299:1: warning: no return statement in function returning non-void [-Wreturn-type] + 1299 | } + | ^ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': +dp_lib/pavie_dp.c:1079:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1079 | system (command); + | ~~~~~~~~^~~~~~~~~ +dp_lib/pavie_dp.c:1081:14: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1081 | system (command); + | ~~~~~~~^~~~~~~~~ + CC util_lib/hsearch.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c +dp_lib/pavie_dp.c: In function 'Alignment* pavie_seq2pavie_msa(Sequence*, char*, char*)': +dp_lib/pavie_dp.c:1365:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1365 | fscanf (fp, "%s", mat); + | ~~~~~~~^~~~~~~~~~~~~~~ fastal/scoring.c: In function 'double calculate_sum_of_pairs_score_affine(char*, int**, double, double)': fastal/scoring.c:76:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | fgets(line, LINE_LENGTH, alignment_file); @@ -895,6 +1070,7 @@ fastal/scoring.c:82:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 82 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/scoring.c: In function 'void compute_ref_alignments(char*, char*, int, int)': fastal/scoring.c:384:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 384 | fgets(line, LINE_LENGTH, seq_file); @@ -909,83 +1085,27 @@ fastal/scoring.c:502:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 502 | system(command); | ~~~~~~^~~~~~~~~ +fastal/parttree.c: In function 'int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)': +fastal/parttree.c:695:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 695 | fgets(line, 500, aln_f); + | ~~~~~^~~~~~~~~~~~~~~~~~ +fastal/parttree.c:701:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 701 | fgets(line, 500, aln_f); + | ~~~~~^~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function 'double agreement_score(char*, char*)': fastal/scoring.c:583:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 583 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +km_coffee/km_coffee.c: In function 'int km_coffee_align3(char*, int, int, char*, char*, int, int, int, char*)': +km_coffee/km_coffee.c:491:14: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 491 | chdir(km_tmp_dir); + | ~~~~~^~~~~~~~~~~~ fastal/scoring.c:584:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 584 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:585:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 585 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from fastal/parttree.c:36: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -dp_lib/util_dp_fasta_nw.c: In function 'int* makepointtable(int*, int*, int)': -dp_lib/util_dp_fasta_nw.c:157:17: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 157 | register int *p; - | ^ -In file included from ./io_lib_header.h:33, - from fastal/iteration.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ - CC km_coffee/kmeans.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/kmeans.deps -c -o km_coffee/kmeans.o km_coffee/kmeans.c - CC t_coffee_lib/t_coffee.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF t_coffee_lib/t_coffee.deps -c -o t_coffee_lib/t_coffee.o t_coffee_lib/t_coffee.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -In file included from ./io_lib_header.h:33, - from dp_lib/CUSTOM_evaluate_for_struc.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from io_lib/tree_util.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -In file included from ./io_lib_header.h:33, - from km_coffee/km_coffee.c:43: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -fastal/parttree.c: In function 'void makepointtable_fast(int*, int, int, int)': -fastal/parttree.c:757:23: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 757 | register int *p; - | ^ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_gotoh_nw.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from fastal/fastal.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ - CC util_lib/aln_compare.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_compare.deps -c -o util_lib/aln_compare.o util_lib/aln_compare.c - CC util_lib/aln_convertion_util.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_convertion_util.deps -c -o util_lib/aln_convertion_util.o util_lib/aln_convertion_util.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -io_lib/tree_util.c: In function 'tnode* tree_scan(Alignment*, NT_node, char*, char*)': -io_lib/tree_util.c:836:26: warning: too many arguments for format [-Wformat-extra-args] - 836 | fprintf (stdout, "Process positions\n", i); - | ^~~~~~~~~~~~~~~~~~~~~ -fastal/parttree.c: In function 'int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)': -fastal/parttree.c:695:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 695 | fgets(line, 500, aln_f); - | ~~~~~^~~~~~~~~~~~~~~~~~ -fastal/parttree.c:701:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 701 | fgets(line, 500, aln_f); - | ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function 'void get_table(short int*, FILE*, long int)': fastal/parttree.c:848:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 848 | fgets(line, LINE_LENGTH, tables_f); @@ -1013,101 +1133,118 @@ fastal/parttree.c:962:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 962 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -dp_lib/util_dp_drivers.c: In function 'Constraint_list* sap_pair(char*, char*, Constraint_list*)': -dp_lib/util_dp_drivers.c:2051:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2051 | register int a; - | ^ -io_lib/tree_util.c: In function 'Alignment* phylotrim(Alignment*, NT_node, char*, char*, char*)': -io_lib/tree_util.c:1299:1: warning: no return statement in function returning non-void [-Wreturn-type] - 1299 | } - | ^ + CC util_lib/random.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/random.deps -c -o util_lib/random.o util_lib/random.c io_lib/tree_util.c: In function 'tnode* no_rec_free_tree(NT_node)': io_lib/tree_util.c:2317:1: warning: no return statement in function returning non-void [-Wreturn-type] 2317 | } | ^ -km_coffee/km_coffee.c: In function 'int km_coffee_align3(char*, int, int, char*, char*, int, int, int, char*)': -km_coffee/km_coffee.c:491:14: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 491 | chdir(km_tmp_dir); - | ~~~~~^~~~~~~~~~~~ -dp_lib/evaluate.c: In function 'Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)': -dp_lib/evaluate.c:3070:67: warning: format '%f' expects argument of type 'double', but argument 4 has type 'int' [-Wformat=] - 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); - | ~~~~^ ~~~ - | | | - | double int - | %3.2d -dp_lib/evaluate.c:3070:81: warning: format '%d' expects argument of type 'int', but argument 5 has type 'double' [-Wformat=] - 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); - | ~~^ ~~~~~~~ - | | | - | int double - | %3f -dp_lib/evaluate.c:3070:93: warning: format '%f' expects argument of type 'double', but argument 6 has type 'int' [-Wformat=] - 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); - | ~~~^ ~~~~~~~~ - | | | - | double int - | %.3d -dp_lib/evaluate.c:3070:109: warning: format '%d' expects argument of type 'int', but argument 7 has type 'double' [-Wformat=] - 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); - | ~~^ ~~~~~~ - | | | - | int double - | %3f -dp_lib/util_dp_gotoh_sw.c: In function 'int gotoh_pair_wise_sw(Alignment*, int*, int**, Constraint_list*)': -dp_lib/util_dp_gotoh_sw.c:391:42: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 391 | fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC util_lib/hsearch.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c - CC util_lib/random.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/random.deps -c -o util_lib/random.o util_lib/random.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC util_lib/reformat.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat.deps -c -o util_lib/reformat.o util_lib/reformat.c + CC util_lib/reformat_struc.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC util_lib/util.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util.deps -c -o util_lib/util.o util_lib/util.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC util_lib/util_aln_analyze.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +fastal/fastal.c: In function 'int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)': +fastal/fastal.c:1924:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1924 | system(blast_command); + | ~~~~~~^~~~~~~~~~~~~~~ +fastal/fastal.c:1929:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1929 | fgets(line, 300, diag_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:1930:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1930 | fgets(line, 300, diag_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:1931:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1931 | fgets(line, 300, diag_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:1976:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1976 | system(blast_command); + | ~~~~~~^~~~~~~~~~~~~~~ +fastal/fastal.c:1980:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1980 | fgets(line, 300, diag_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:1981:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1981 | fgets(line, 300, diag_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:1982:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1982 | fgets(line, 300, diag_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/fastal.c: In function 'int seq_pair2blat_diagonal(char*, char*, int**, int*, int, int, int)': +fastal/fastal.c:2115:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2115 | system(blast_command); + | ~~~~~~^~~~~~~~~~~~~~~ + CC util_lib/util_analyse_constraints_list.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_analyse_constraints_list.deps -c -o util_lib/util_analyse_constraints_list.o util_lib/util_analyse_constraints_list.c +fastal/fastal.c: In function 'int seq_pair2blastz_diagonal(char*, char*, int**, int*, int, int, int)': +fastal/fastal.c:2262:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2262 | system(blast_command); + | ~~~~~~^~~~~~~~~~~~~~~ io_lib/tree_util.c: In function 'int node_sort(char*, NT_node)': io_lib/tree_util.c:6273:1: warning: no return statement in function returning non-void [-Wreturn-type] 6273 | } | ^ -dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': -dp_lib/pavie_dp.c:1078:33: warning: '%s' directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] - 1078 | sprintf ( command, "cp %s %s", mat_name[a], latest); - | ^~ ~~~~~~ -In file included from /usr/include/stdio.h:970, - from dp_lib/pavie_dp.c:27: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)' at dp_lib/pavie_dp.c:1078:15: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 1004) into a destination of size 1000 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ io_lib/tree_util.c: In function 'int treelist2leafgroup(Sequence*, Sequence*, char*)': io_lib/tree_util.c:6566:1: warning: no return statement in function returning non-void [-Wreturn-type] 6566 | } | ^ -dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': -dp_lib/pavie_dp.c:1080:30: warning: '%s' directive writing up to 999 bytes into a region of size 997 [-Wformat-overflow=] - 1080 | sprintf ( command, "cp %s %s", latest, current); - | ^~ ~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)' at dp_lib/pavie_dp.c:1080:15: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 2003 bytes into a destination of size 1000 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ io_lib/tree_util.c: In function 'int count_tree_groups(Sequence*, char*)': io_lib/tree_util.c:6669:1: warning: no return statement in function returning non-void [-Wreturn-type] 6669 | } | ^ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -fastal/iteration.c: In function 'void split_set(FILE*, Fastal_profile*, Fastal_profile*, char*, int, int*, char*)': -fastal/iteration.c:185:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 185 | fgets(line, LINE_LENGTH , alignment_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +fastal/fastal.c: In function 'void file_pos2profile(FILE*, long int, Fastal_profile*, int, Fastal_param*)': +fastal/fastal.c:3201:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3201 | fgets (line, LINE_LENGTH , seq_file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c: In function 'void profile_file2profile(Fastal_profile*, FILE*, long int, Fastal_param*)': +fastal/fastal.c:3323:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3323 | fgets(line, LINE_LENGTH, profile_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3326:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3326 | fgets(line, LINE_LENGTH, profile_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3329:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3329 | fgets(line, LINE_LENGTH, profile_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3331:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3331 | fgets(line, LINE_LENGTH, profile_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3333:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3333 | fgets(line, LINE_LENGTH, profile_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3352:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3352 | fgets(line, LINE_LENGTH , profile_f); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c: In function 'void edit_seq2aligned_seq(char*, FILE*, long int, FILE*)': +fastal/fastal.c:3502:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3502 | fgets (line, LINE_LENGTH , sequence_file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c: In function 'void edit2alignment(FILE*, long int*, FILE*, long int*, int, int, char*, int, FILE*, int, FILE*)': +fastal/fastal.c:3575:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3575 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3577:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3577 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3579:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3579 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3581:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3581 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3643:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3643 | fgets(aligned_sequence, alignment_length+3, edit_seq_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC util_lib/util_constraints_list.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_constraints_list.deps -c -o util_lib/util_constraints_list.o util_lib/util_constraints_list.c io_lib/tree_util.c: In function 'int treelist2splits(Sequence*, Sequence*)': io_lib/tree_util.c:7047:1: warning: no return statement in function returning non-void [-Wreturn-type] 7047 | } @@ -1116,63 +1253,11 @@ io_lib/tree_util.c:7131:1: warning: no return statement in function returning non-void [-Wreturn-type] 7131 | } | ^ -fastal/iteration.c: In function 'void iterate(Fastal_param*, void*, char*, char*, int)': -fastal/iteration.c:310:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 310 | fgets(line, LINE_LENGTH , alignment_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:435:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 435 | system(command); - | ~~~~~~^~~~~~~~~ -fastal/iteration.c: In function 'void write_iterated_aln(char*, char*, char*, char*, int*, int, char*, int*, int)': -fastal/iteration.c:501:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 501 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:504:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 504 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:535:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 535 | fgets(alnline, ALNLINE_LENGTH, old_aln_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ io_lib/tree_util.c: In function 'int treelist2frame(Sequence*, Sequence*)': io_lib/tree_util.c:7204:1: warning: no return statement in function returning non-void [-Wreturn-type] 7204 | } | ^ -fastal/iteration.c: In function 'void edit2seq_pattern(FILE*, char*, char*)': -fastal/iteration.c:563:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:565:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 565 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:567:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 567 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:569:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 569 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC util_lib/reformat.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat.deps -c -o util_lib/reformat.o util_lib/reformat.c - CC util_lib/reformat_struc.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -io_lib/tree_util.c: In function 'char* graph2cons_d(long unsigned int, int)': -io_lib/tree_util.c:10163:27: warning: NULL used in arithmetic [-Wpointer-arith] -10163 | while ((c=rn_c(s))!=NULL) - | ^~~~ -io_lib/tree_util.c: In function 'long unsigned int insert_gap_in_graph_d(long unsigned int)': -io_lib/tree_util.c:10181:20: warning: converting to non-pointer type 'long unsigned int' from NULL [-Wconversion-null] -10181 | unsigned long pn=NULL; - | ^~~~ -io_lib/tree_util.c:10183:22: warning: converting to non-pointer type 'long unsigned int' from NULL [-Wconversion-null] -10183 | if (!start) return NULL; - | ^~~~ -io_lib/tree_util.c:10196:14: warning: passing NULL to non-pointer argument 2 of 'void wn_c(long unsigned int, long unsigned int)' [-Wconversion-null] -10196 | wn_c(n,NULL); - | ^~~~ -io_lib/tree_util.c:9947:46: note: declared here - 9947 | void wn_c (unsigned long n, unsigned long t); - | ~~~~~~~~~~~~~~^ dp_lib/util_dp_drivers.c: In function 'char* seq_file2msa_file(char*, char*, char*)': dp_lib/util_dp_drivers.c:1014:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1014 | chdir (dir); @@ -1227,47 +1312,14 @@ dp_lib/util_dp_drivers.c:1774:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1774 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c: In function 'int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)': -fastal/fastal.c:1924:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1924 | system(blast_command); - | ~~~~~~^~~~~~~~~~~~~~~ -fastal/fastal.c:1929:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1929 | fgets(line, 300, diag_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:1930:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1930 | fgets(line, 300, diag_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:1931:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1931 | fgets(line, 300, diag_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:1976:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1976 | system(blast_command); - | ~~~~~~^~~~~~~~~~~~~~~ -fastal/fastal.c:1980:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1980 | fgets(line, 300, diag_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:1981:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1981 | fgets(line, 300, diag_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:1982:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1982 | fgets(line, 300, diag_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* thread_pair(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1906:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1906 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c: In function 'int seq_pair2blat_diagonal(char*, char*, int**, int*, int, int, int)': -fastal/fastal.c:2115:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2115 | system(blast_command); - | ~~~~~~^~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* lsqman_pair(char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1981:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1981 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c: In function 'int seq_pair2blastz_diagonal(char*, char*, int**, int*, int, int, int)': -fastal/fastal.c:2262:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2262 | system(blast_command); - | ~~~~~~^~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function 'Constraint_list* sap_pair(char*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:2073:17: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2073 | atoi(strtok (seq,SEPARATORS)); @@ -1285,6 +1337,23 @@ dp_lib/util_dp_drivers.c:2256:13: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2256 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +io_lib/tree_util.c: In function 'char* graph2cons_d(long unsigned int, int)': +io_lib/tree_util.c:10163:27: warning: NULL used in arithmetic [-Wpointer-arith] +10163 | while ((c=rn_c(s))!=NULL) + | ^~~~ +io_lib/tree_util.c: In function 'long unsigned int insert_gap_in_graph_d(long unsigned int)': +io_lib/tree_util.c:10181:20: warning: converting to non-pointer type 'long unsigned int' from NULL [-Wconversion-null] +10181 | unsigned long pn=NULL; + | ^~~~ +io_lib/tree_util.c:10183:22: warning: converting to non-pointer type 'long unsigned int' from NULL [-Wconversion-null] +10183 | if (!start) return NULL; + | ^~~~ +io_lib/tree_util.c:10196:14: warning: passing NULL to non-pointer argument 2 of 'void wn_c(long unsigned int, long unsigned int)' [-Wconversion-null] +10196 | wn_c(n,NULL); + | ^~~~ +io_lib/tree_util.c:9947:46: note: declared here + 9947 | void wn_c (unsigned long n, unsigned long t); + | ~~~~~~~~~~~~~~^ dp_lib/evaluate.c: In function 'Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)': dp_lib/evaluate.c:809:26: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 809 | fscanf (fp, "%d ", &res); @@ -1295,109 +1364,80 @@ dp_lib/evaluate.c:819:18: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 819 | fscanf (fp, "%f %f", &sseq, &mseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c: In function 'void file_pos2profile(FILE*, long int, Fastal_profile*, int, Fastal_param*)': -fastal/fastal.c:3201:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3201 | fgets (line, LINE_LENGTH , seq_file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c: In function 'void profile_file2profile(Fastal_profile*, FILE*, long int, Fastal_param*)': -fastal/fastal.c:3323:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3323 | fgets(line, LINE_LENGTH, profile_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3326:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3326 | fgets(line, LINE_LENGTH, profile_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3329:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3329 | fgets(line, LINE_LENGTH, profile_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3331:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3331 | fgets(line, LINE_LENGTH, profile_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3333:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3333 | fgets(line, LINE_LENGTH, profile_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3352:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3352 | fgets(line, LINE_LENGTH , profile_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c: In function 'void edit_seq2aligned_seq(char*, FILE*, long int, FILE*)': -fastal/fastal.c:3502:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3502 | fgets (line, LINE_LENGTH , sequence_file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c: In function 'void edit2alignment(FILE*, long int*, FILE*, long int*, int, int, char*, int, FILE*, int, FILE*)': -fastal/fastal.c:3575:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3575 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3577:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3577 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3579:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3579 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3581:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3581 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3643:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3643 | fgets(aligned_sequence, alignment_length+3, edit_seq_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/scoring.c: In function 'int complete_agreement_score(char*, const char*)': -fastal/scoring.c:624:49: warning: '%s' directive writing up to 499 bytes into a region of size 200 [-Wformat-overflow=] - 624 | sprintf(ref_file_name, "%s/%s",directory, dp->d_name); - | ^~ ~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from fastal/scoring.c:28: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'int complete_agreement_score(char*, const char*)' at fastal/scoring.c:624:11: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 756 bytes into a destination of size 200 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -km_coffee/km_util.c: In function 'char* my_make_temp_dir(char*, char*)': -km_coffee/km_util.c:96:69: warning: format '%s' expects a matching 'char*' argument [-Wformat=] - 96 | fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); - | ~^ - | | - | char* -io_lib/tree_util.c: In function 'FILE* create_tree(NT_node, NT_node, int*, int*, int*, tnode***, FILE*)': -io_lib/tree_util.c:3973:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3973 | fscanf(fp,"%f",&dist); - | ~~~~~~^~~~~~~~~~~~~~~ -io_lib/tree_util.c:3981:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3981 | fscanf(fp,"%f",&bootstrap); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~ - CC util_lib/util.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util.deps -c -o util_lib/util.o util_lib/util.c - CC util_lib/util_aln_analyze.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c - CC util_lib/util_analyse_constraints_list.c +In file included from ./io_lib_header.h:33, + from t_coffee_lib/t_coffee.c:35: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ + CC util_lib/util_declare.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_analyse_constraints_list.deps -c -o util_lib/util_analyse_constraints_list.o util_lib/util_analyse_constraints_list.c - CC util_lib/util_constraints_list.c + CC util_lib/util_domain_constraints_list.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_domain_constraints_list.deps -c -o util_lib/util_domain_constraints_list.o util_lib/util_domain_constraints_list.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, from util_lib/aln_compare.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_constraints_list.deps -c -o util_lib/util_constraints_list.o util_lib/util_constraints_list.c + CC util_lib/util_dps.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_dps.deps -c -o util_lib/util_dps.o util_lib/util_dps.c + CC util_lib/util_job_handling.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_job_handling.deps -c -o util_lib/util_job_handling.o util_lib/util_job_handling.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/evaluate.c: In function 'float** initialise_aa_physico_chemical_property_table(int*)': dp_lib/evaluate.c:7626:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 7626 | fscanf (fp, "%f %c %*s",&v1, &c1 ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -io_lib/tree_util.c: In function 'int check_node(ALN_node, char*)': -io_lib/tree_util.c:9772:1: warning: control reaches end of non-void function [-Wreturn-type] - 9772 | } +io_lib/tree_util.c: In function 'FILE* create_tree(NT_node, NT_node, int*, int*, int*, tnode***, FILE*)': +io_lib/tree_util.c:3973:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3973 | fscanf(fp,"%f",&dist); + | ~~~~~~^~~~~~~~~~~~~~~ +io_lib/tree_util.c:3981:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3981 | fscanf(fp,"%f",&bootstrap); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~ +dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': +dp_lib/pavie_dp.c:1078:33: warning: '%s' directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] + 1078 | sprintf ( command, "cp %s %s", mat_name[a], latest); + | ^~ ~~~~~~ +In file included from /usr/include/stdio.h:970, + from dp_lib/pavie_dp.c:27: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)' at dp_lib/pavie_dp.c:1078:15: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 1004) into a destination of size 1000 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': +dp_lib/pavie_dp.c:1080:30: warning: '%s' directive writing up to 999 bytes into a region of size 997 [-Wformat-overflow=] + 1080 | sprintf ( command, "cp %s %s", latest, current); + | ^~ ~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)' at dp_lib/pavie_dp.c:1080:15: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 2003 bytes into a destination of size 1000 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +t_coffee_lib/t_coffee.c: In function 'char** km_coffee(int, char**)': +t_coffee_lib/t_coffee.c:6577:1: warning: no return statement in function returning non-void [-Wreturn-type] + 6577 | } | ^ +t_coffee_lib/t_coffee.c: In function 'Alignment* t_coffee_dpa(int, char**)': +t_coffee_lib/t_coffee.c:7172:57: warning: too many arguments for format [-Wformat-extra-args] + 7172 | else { w=seq2dpa_weight (S, "longuest");fprintf ( le, "default longuest\n", dpa_weight);} + | ^~~~~~~~~~~~~~~~~~~~ + CC util_lib/util_make_tree.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_make_tree.deps -c -o util_lib/util_make_tree.o util_lib/util_make_tree.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, - from t_coffee_lib/t_coffee.c:35: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/aln_convertion_util.c:33: + from util_lib/hsearch.c:35: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ @@ -1408,73 +1448,110 @@ | | | | int size_t {aka long unsigned int} | %li +io_lib/tree_util.c: In function 'int check_node(ALN_node, char*)': +io_lib/tree_util.c:9772:1: warning: control reaches end of non-void function [-Wreturn-type] + 9772 | } + | ^ In file included from ./io_lib_header.h:33, - from util_lib/hsearch.c:35: + from util_lib/aln_convertion_util.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -t_coffee_lib/t_coffee.c: In function 'char** km_coffee(int, char**)': -t_coffee_lib/t_coffee.c:6577:1: warning: no return statement in function returning non-void [-Wreturn-type] - 6577 | } - | ^ -util_lib/aln_convertion_util.c: In function 'int trim_aln_file(char*, char*, char*, char*)': -util_lib/aln_convertion_util.c:3105:62: warning: NULL used in arithmetic [-Wpointer-arith] - 3105 | while ((get_next_fasta_sequence(fp, &name, &comment,&seq)!=NULL)) - | ^~~~ +fastal/scoring.c: In function 'int complete_agreement_score(char*, const char*)': +fastal/scoring.c:624:49: warning: '%s' directive writing up to 499 bytes into a region of size 200 [-Wformat-overflow=] + 624 | sprintf(ref_file_name, "%s/%s",directory, dp->d_name); + | ^~ ~~~~~~~~~ +In file included from /usr/include/stdio.h:970, + from fastal/scoring.c:28: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int complete_agreement_score(char*, const char*)' at fastal/scoring.c:624:11: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 756 bytes into a destination of size 200 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from util_lib/reformat_struc.c:34: + from util_lib/util_aln_analyze.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC util_lib/util_declare.c -t_coffee_lib/t_coffee.c: In function 'Alignment* t_coffee_dpa(int, char**)': -t_coffee_lib/t_coffee.c:7172:57: warning: too many arguments for format [-Wformat-extra-args] - 7172 | else { w=seq2dpa_weight (S, "longuest");fprintf ( le, "default longuest\n", dpa_weight);} - | ^~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c - CC util_lib/util_domain_constraints_list.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_domain_constraints_list.deps -c -o util_lib/util_domain_constraints_list.o util_lib/util_domain_constraints_list.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -util_lib/aln_convertion_util.c: In function 'Alignment* aln2conservation(Alignment*, int, char*)': -util_lib/aln_convertion_util.c:4511:1: warning: no return statement in function returning non-void [-Wreturn-type] - 4511 | } - | ^ -util_lib/reformat_struc.c: In function 'void bfactor2x_in_pdb(char*, char*, float*)': -util_lib/reformat_struc.c:125:25: warning: too many arguments for format [-Wformat-extra-args] - 125 | fprintf (out, "ATOM ", lw[1]);//ATOM - | ^~~~~~~~ In file included from ./io_lib_header.h:33, - from util_lib/util_constraints_list.c:37: + from util_lib/reformat.c:35: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from util_lib/reformat_struc.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -util_lib/aln_convertion_util.c: In function 'Alignment* aln2N_replicate(Alignment*, char*, char*)': -util_lib/aln_convertion_util.c:7762:1: warning: no return statement in function returning non-void [-Wreturn-type] - 7762 | } - | ^ t_coffee_lib/t_coffee.c: In function 'int run_other_pg(int, char**)': t_coffee_lib/t_coffee.c:6139:30: warning: control reaches end of non-void function [-Wreturn-type] 6139 | unpack_all_perl_script (argv[0]+strlen ("unpack_")); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ./io_lib_header.h:33, + from util_lib/util_analyse_constraints_list.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ t_coffee_lib/t_coffee.c: In function 'Alignment* km_align_seq_slow(char*, Alignment*, int, char**, int, int)': t_coffee_lib/t_coffee.c:6816:1: warning: control reaches end of non-void function [-Wreturn-type] 6816 | } | ^ In file included from ./io_lib_header.h:33, - from util_lib/util_analyse_constraints_list.c:33: + from util_lib/util.c:52: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -util_lib/util_constraints_list.c: In function 'Constraint_list* unfreeze_constraint_list(Constraint_list*)': -util_lib/util_constraints_list.c:1311:1: warning: no return statement in function returning non-void [-Wreturn-type] - 1311 | } +In file included from ./io_lib_header.h:33, + from util_lib/util_constraints_list.c:37: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +util_lib/util_aln_analyze.c: In function 'Alignment* sar_analyze(Alignment*, Alignment*, char*)': +util_lib/util_aln_analyze.c:713:1: warning: no return statement in function returning non-void [-Wreturn-type] + 713 | } + | ^ +util_lib/aln_convertion_util.c: In function 'int trim_aln_file(char*, char*, char*, char*)': +util_lib/aln_convertion_util.c:3105:62: warning: NULL used in arithmetic [-Wpointer-arith] + 3105 | while ((get_next_fasta_sequence(fp, &name, &comment,&seq)!=NULL)) + | ^~~~ +util_lib/reformat_struc.c: In function 'void bfactor2x_in_pdb(char*, char*, float*)': +util_lib/reformat_struc.c:125:25: warning: too many arguments for format [-Wformat-extra-args] + 125 | fprintf (out, "ATOM ", lw[1]);//ATOM + | ^~~~~~~~ +util_lib/aln_convertion_util.c: In function 'Alignment* aln2conservation(Alignment*, int, char*)': +util_lib/aln_convertion_util.c:4511:1: warning: no return statement in function returning non-void [-Wreturn-type] + 4511 | } | ^ In file included from ./io_lib_header.h:33, - from util_lib/util_aln_analyze.c:33: + from util_lib/util_domain_constraints_list.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +util_lib/util.c: In function 'int cherry(int, char**)': +util_lib/util.c:1009:1: warning: no return statement in function returning non-void [-Wreturn-type] + 1009 | } + | ^ +In file included from ./io_lib_header.h:33, + from util_lib/util_declare.c:37: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ +util_lib/aln_convertion_util.c: In function 'Alignment* aln2N_replicate(Alignment*, char*, char*)': +util_lib/aln_convertion_util.c:7762:1: warning: no return statement in function returning non-void [-Wreturn-type] + 7762 | } + | ^ +util_lib/util_aln_analyze.c: In function 'Alignment* or_scan(Alignment*, Alignment*, char*)': +util_lib/util_aln_analyze.c:4480:1: warning: no return statement in function returning non-void [-Wreturn-type] + 4480 | } + | ^ +util_lib/util_constraints_list.c: In function 'Constraint_list* unfreeze_constraint_list(Constraint_list*)': +util_lib/util_constraints_list.c:1311:1: warning: no return statement in function returning non-void [-Wreturn-type] + 1311 | } + | ^ util_lib/reformat_struc.c: In function 'Ca_trace* simple_read_ca_trace(char*)': util_lib/reformat_struc.c:370:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 370 | fscanf ( fp, "%*s" ); @@ -1502,47 +1579,37 @@ util_lib/util_constraints_list.c:2851:40: warning: too many arguments for format [-Wformat-extra-args] 2851 | x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); | ^~~~~~~~~~~~~~~~~~~ -util_lib/util_aln_analyze.c: In function 'Alignment* sar_analyze(Alignment*, Alignment*, char*)': -util_lib/util_aln_analyze.c:713:1: warning: no return statement in function returning non-void [-Wreturn-type] - 713 | } - | ^ In file included from ./io_lib_header.h:33, - from util_lib/reformat.c:35: + from util_lib/util_dps.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC util_lib/util_dps.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_dps.deps -c -o util_lib/util_dps.o util_lib/util_dps.c In file included from ./io_lib_header.h:33, - from util_lib/util.c:52: + from util_lib/util_job_handling.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -util_lib/util_aln_analyze.c: In function 'Alignment* or_scan(Alignment*, Alignment*, char*)': -util_lib/util_aln_analyze.c:4480:1: warning: no return statement in function returning non-void [-Wreturn-type] - 4480 | } +util_lib/util.c: In function 'int dump_nfc(char*, char*)': +util_lib/util.c:4456:1: warning: no return statement in function returning non-void [-Wreturn-type] + 4456 | } | ^ - CC util_lib/util_job_handling.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_job_handling.deps -c -o util_lib/util_job_handling.o util_lib/util_job_handling.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC util_lib/util_make_tree.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_make_tree.deps -c -o util_lib/util_make_tree.o util_lib/util_make_tree.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -util_lib/aln_convertion_util.c: In function 'Alignment* extract_aln3(Alignment*, char*)': -util_lib/aln_convertion_util.c:7524:16: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 7524 | fgets ( line, VERY_LONG_STRING,fp); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/aln_convertion_util.c:7543:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 7543 | if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/aln_convertion_util.c:7547:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 7547 | fgets ( line, VERY_LONG_STRING,fp); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'int cherry(int, char**)': -util_lib/util.c:1009:1: warning: no return statement in function returning non-void [-Wreturn-type] - 1009 | } +util_lib/reformat.c: In function 'int output_suchard_aln(char*, Alignment*)': +util_lib/reformat.c:7551:1: warning: no return statement in function returning non-void [-Wreturn-type] + 7551 | } + | ^ +util_lib/util.c: In function 'int set_nproc(int)': +util_lib/util.c:5489:1: warning: no return statement in function returning non-void [-Wreturn-type] + 5489 | } + | ^ +util_lib/util.c: In function 'char* vremove3(char*, char*)': +util_lib/util.c:6938:1: warning: no return statement in function returning non-void [-Wreturn-type] + 6938 | } | ^ +In file included from ./io_lib_header.h:33, + from util_lib/util_make_tree.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ util_lib/util_constraints_list.c: In function 'Job_TC* submit_lib_job(Job_TC*)': util_lib/util_constraints_list.c:582:19: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 582 | chdir (tdir); @@ -1558,6 +1625,16 @@ util_lib/util_constraints_list.c:1193:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1193 | fgets ( line,LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +util_lib/aln_convertion_util.c: In function 'Alignment* extract_aln3(Alignment*, char*)': +util_lib/aln_convertion_util.c:7524:16: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 7524 | fgets ( line, VERY_LONG_STRING,fp); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/aln_convertion_util.c:7543:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 7543 | if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/aln_convertion_util.c:7547:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 7547 | fgets ( line, VERY_LONG_STRING,fp); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'int read_cpu_in_list(char*)': util_lib/util_constraints_list.c:2599:27: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2599 | if ( c=='C')fscanf( fp, "PU %d\n", &cpu); @@ -1569,6 +1646,10 @@ util_lib/util_constraints_list.c:2922:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2922 | fscanf (fp, "%*s %d %*s\n", &l); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util_make_tree.c: In function 'tnode* redundate(Sequence*, NT_node, char*, char*)': +util_lib/util_make_tree.c:66:1: warning: no return statement in function returning non-void [-Wreturn-type] + 66 | } + | ^ util_lib/util_constraints_list.c:2954:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2954 | fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1579,73 +1660,10 @@ util_lib/util_constraints_list.c:4053:40: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4053 | fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'int dump_nfc(char*, char*)': -util_lib/util.c:4456:1: warning: no return statement in function returning non-void [-Wreturn-type] - 4456 | } - | ^ -util_lib/util.c: In function 'int set_nproc(int)': -util_lib/util.c:5489:1: warning: no return statement in function returning non-void [-Wreturn-type] - 5489 | } - | ^ -util_lib/reformat.c: In function 'int output_suchard_aln(char*, Alignment*)': -util_lib/reformat.c:7551:1: warning: no return statement in function returning non-void [-Wreturn-type] - 7551 | } - | ^ -util_lib/util.c: In function 'char* vremove3(char*, char*)': -util_lib/util.c:6938:1: warning: no return statement in function returning non-void [-Wreturn-type] - 6938 | } - | ^ -dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': -dp_lib/util_dp_drivers.c:382:31: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - 382 | sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); - | ^~ -In file included from /usr/include/stdio.h:970, - from dp_lib/util_dp_drivers.c:27: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:382:16: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': -dp_lib/util_dp_drivers.c:373:30: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - 373 | sprintf ( mat, "%s", (strm(m, "default"))?"blosum62mt":m); - | ^~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:373:15: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': -dp_lib/util_dp_drivers.c:386:41: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - 386 | if ( M->matrix[0])sprintf ( mat, "%s", M->matrix); - | ^~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:386:33: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/util_declare.c:37: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/util_domain_constraints_list.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ +util_lib/util_make_tree.c: In function 'void fast_nj_tree(char**)': +util_lib/util_make_tree.c:853:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 853 | register int i; + | ^ util_lib/util.c: In function 'FILE* hsort_file(FILE*, int, int, size_t, int, int, int (*)(const void*, const void*, int, int, size_t), void* (*)(void*, void*, size_t))': util_lib/util.c:281:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 281 | fread( rra, size, len,fp); /*rra=ra[--l]*/ @@ -1666,24 +1684,14 @@ util_lib/util.c:420:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 420 | fread ( key2, el_size, entry_len,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/util_job_handling.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -util_lib/util.c: In function 'FILE* get_number_list_in_file(FILE*, int*, int*, int*)': -util_lib/util.c:847:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 847 | fscanf ( fp, "%d",&list[n[0]++]); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int output_header_mat(int**, char*)': util_lib/reformat.c:14453:1: warning: no return statement in function returning non-void [-Wreturn-type] 14453 | } | ^ -In file included from ./io_lib_header.h:33, - from util_lib/util_make_tree.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ +util_lib/util.c: In function 'FILE* get_number_list_in_file(FILE*, int*, int*, int*)': +util_lib/util.c:847:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 847 | fscanf ( fp, "%d",&list[n[0]++]); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'int quantile(int, char**)': util_lib/util.c:1321:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1321 | fscanf ( fp, "%s %s\n", s1, s2); @@ -1701,23 +1709,108 @@ util_lib/util.c:1813:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1813 | fscanf (fp, "\n"); | ~~~~~~~^~~~~~~~~~ +util_lib/util_make_tree.c: In function 'char* seq2co_aln_file(char*, char*)': +util_lib/util_make_tree.c:124:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 124 | chdir (dir); + | ~~~~~~^~~~~ +util_lib/util_make_tree.c:127:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 127 | chdir (cdir); + | ~~~~~~~~~^~~~~~ +util_lib/util_make_tree.c: In function 'char* seq2mafft_aln_file(char*, char*)': +util_lib/util_make_tree.c:157:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 157 | chdir (dir); + | ~~~~~~^~~~~ +util_lib/util_make_tree.c:160:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 160 | chdir (cdir); + | ~~~~~~~~~^~~~~~ +util_lib/util_make_tree.c: In function 'char* seq2cw_aln_file(char*, char*)': +util_lib/util_make_tree.c:190:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 190 | chdir (dir); + | ~~~~~~^~~~~ +util_lib/util_make_tree.c:192:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 192 | chdir (cdir); + | ~~~~~~~~~^~~~~~ +util_lib/util_make_tree.c: In function 'char* prf_pair2cw_aln_file(char*, char*, char*)': +util_lib/util_make_tree.c:223:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 223 | chdir (dir); + | ~~~~~~^~~~~ +util_lib/util_make_tree.c:226:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 226 | chdir (cdir); + | ~~~~~~~~~^~~~~~ util_lib/util.c: In function 'int perl_strstr(char*, char*)': util_lib/util.c:2468:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2468 | fscanf (fp, "%d", &r); | ~~~~~~~^~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/util_dps.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -util_lib/util_make_tree.c: In function 'tnode* redundate(Sequence*, NT_node, char*, char*)': -util_lib/util_make_tree.c:66:1: warning: no return statement in function returning non-void [-Wreturn-type] - 66 | } - | ^ -util_lib/util_make_tree.c: In function 'void fast_nj_tree(char**)': -util_lib/util_make_tree.c:853:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 853 | register int i; - | ^ +util_lib/util_make_tree.c: In function 'tnode* seq2fftns1_dnd(Sequence*)': +util_lib/util_make_tree.c:1855:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1855 | chdir (dir); + | ~~~~~~^~~~~ +util_lib/util_make_tree.c:1868:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1868 | chdir (cdir); + | ~~~~~~~~~^~~~~~ +util_lib/util_make_tree.c: In function 'tnode* seq2fftns2_dnd(Sequence*)': +util_lib/util_make_tree.c:1884:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1884 | chdir (dir); + | ~~~~~~^~~~~ +util_lib/util_make_tree.c:1897:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1897 | chdir (cdir); + | ~~~~~~~~~^~~~~~ +util_lib/util_make_tree.c: In function 'tnode* seq2mafft_dnd(Sequence*)': +util_lib/util_make_tree.c:1913:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1913 | chdir (dir); + | ~~~~~~^~~~~ +util_lib/util_make_tree.c:1926:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1926 | chdir (cdir); + | ~~~~~~~~~^~~~~~ +util_lib/util_make_tree.c: In function 'tnode* seq2parttree_dnd(Sequence*)': +util_lib/util_make_tree.c:1943:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1943 | chdir (dir); + | ~~~~~~^~~~~ +util_lib/util_make_tree.c:1956:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1956 | chdir (cdir); + | ~~~~~~~~~^~~~~~ +util_lib/util_make_tree.c: In function 'tnode* seq2dpparttree_dnd(Sequence*)': +util_lib/util_make_tree.c:1973:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1973 | chdir (dir); + | ~~~~~~^~~~~ +util_lib/util_make_tree.c:1988:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1988 | chdir (cdir); + | ~~~~~~~~~^~~~~~ +util_lib/util_make_tree.c: In function 'tnode* seq2fastparttree_dnd(Sequence*)': +util_lib/util_make_tree.c:2006:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2006 | chdir (dir); + | ~~~~~~^~~~~ +util_lib/util_make_tree.c:2019:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2019 | chdir (cdir); + | ~~~~~~~~~^~~~~~ +util_lib/util_make_tree.c: In function 'tnode* seq2cwquick_dnd(Sequence*)': +util_lib/util_make_tree.c:2035:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2035 | chdir (dir); + | ~~~~~~^~~~~ +util_lib/util_make_tree.c:2043:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2043 | chdir (cdir); + | ~~~~~~~~~^~~~~~ +util_lib/util_make_tree.c: In function 'tnode* seq2cw_dnd(Sequence*)': +util_lib/util_make_tree.c:2060:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2060 | chdir (dir); + | ~~~~~~^~~~~ +util_lib/util_make_tree.c:2068:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2068 | chdir (cdir); + | ~~~~~~~~~^~~~~~ +util_lib/util_make_tree.c: In function 'tnode* aln2cw_tree(Alignment*)': +util_lib/util_make_tree.c:2088:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2088 | chdir (dir); + | ~~~~~~^~~~~ +util_lib/util_make_tree.c:2095:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2095 | chdir (cdir); + | ~~~~~~~~~^~~~~~ +util_lib/util_make_tree.c: In function 'tnode* seq2cw_tree(Sequence*)': +util_lib/util_make_tree.c:2110:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2110 | chdir (dir); + | ~~~~~~^~~~~ +util_lib/util_make_tree.c:2119:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2119 | chdir (cdir); + | ~~~~~~~~~^~~~~~ util_lib/util.c: In function 'int printf_system_direct_check(char*, ...)': util_lib/util.c:4440:19: warning: control reaches end of non-void function [-Wreturn-type] 4440 | printf_exit ( EXIT_FAILURE, stderr, "ERROR: Could not run %s\n", buf); @@ -1784,6 +1877,10 @@ util_lib/reformat.c:1493:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1493 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'int get_cl_param(int, char**, FILE**, const char*, int*, const char*, int, int, const char*, ...)': +util_lib/util.c:7645:9: warning: second parameter of 'va_start' not last named argument [-Wvarargs] + 7645 | va_start (ap, usage); + | ^~~~~~~~ util_lib/reformat.c: In function 'int is_pdb_name(char*)': util_lib/reformat.c:1788:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1788 | fscanf ( fp, "%d", &result); @@ -1792,27 +1889,6 @@ util_lib/reformat.c:1826:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1826 | fscanf ( fp, "\n%s\n", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -dp_lib/util_dp_drivers.c: In function 'Alignment* realign_block(Alignment*, int, int, char*)': -dp_lib/util_dp_drivers.c:921:25: warning: ' -infile=' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] - 921 | sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); - | ^~~~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Alignment* realign_block(Alignment*, int, int, char*)' at dp_lib/util_dp_drivers.c:921:11: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 38 or more bytes (assuming 1037) into a destination of size 1000 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -util_lib/reformat.c: In function 'int fast_format_determination(char*)': -util_lib/reformat.c:2507:1: warning: control reaches end of non-void function [-Wreturn-type] - 2507 | } - | ^ -util_lib/util.c: In function 'int get_cl_param(int, char**, FILE**, const char*, int*, const char*, int, int, const char*, ...)': -util_lib/util.c:7645:9: warning: second parameter of 'va_start' not last named argument [-Wvarargs] - 7645 | va_start (ap, usage); - | ^~~~~~~~ util_lib/util.c: In function 'char** get_parameter(char*, int*, char*)': util_lib/util.c:7912:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7912 | fgets ( line, VERY_LONG_STRING,fp); @@ -1821,6 +1897,10 @@ util_lib/util.c:7932:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 7932 | fscanf ( fp, "%s", string); | ~~~~~~~^~~~~~~~~~~~~~~~~~~ +util_lib/reformat.c: In function 'int fast_format_determination(char*)': +util_lib/reformat.c:2507:1: warning: control reaches end of non-void function [-Wreturn-type] + 2507 | } + | ^ util_lib/util.c: In function 'int** get_file_block_pattern(char*, int*, int)': util_lib/util.c:8319:25: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 8319 | fgets ( line, lline,fp); @@ -1836,6 +1916,10 @@ util_lib/util.c:8528:10: warning: control reaches end of non-void function [-Wreturn-type] 8528 | myexit (EXIT_FAILURE); | ~~~~~~~^~~~~~~~~~~~~~ +util_lib/util.c: In function 'int km_main(int, char**)': +util_lib/util.c:10533:1: warning: control reaches end of non-void function [-Wreturn-type] +10533 | } + | ^ util_lib/reformat.c: In function 'Weights* get_amps_sd_scores(char*)': util_lib/reformat.c:3948:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3948 | fscanf ( fp, "%s", buf2); @@ -1884,10 +1968,6 @@ util_lib/reformat.c:5264:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 5264 | fgets (line, ml,fp); | ~~~~~~^~~~~~~~~~~~~ -util_lib/util.c: In function 'int km_main(int, char**)': -util_lib/util.c:10533:1: warning: control reaches end of non-void function [-Wreturn-type] -10533 | } - | ^ util_lib/reformat.c: In function 'int fscanf_seq_name(FILE*, char*)': util_lib/reformat.c:5724:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 5724 | fscanf (fp, "%s", name); @@ -1911,104 +1991,47 @@ util_lib/reformat.c:6511:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 6511 | fscanf (fp, "%s %d", name,&i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -util_lib/util_make_tree.c: In function 'char* seq2co_aln_file(char*, char*)': -util_lib/util_make_tree.c:124:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 124 | chdir (dir); - | ~~~~~~^~~~~ -util_lib/util_make_tree.c:127:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 127 | chdir (cdir); - | ~~~~~~~~~^~~~~~ -util_lib/util_make_tree.c: In function 'char* seq2mafft_aln_file(char*, char*)': -util_lib/util_make_tree.c:157:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 157 | chdir (dir); - | ~~~~~~^~~~~ -util_lib/util_make_tree.c:160:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 160 | chdir (cdir); - | ~~~~~~~~~^~~~~~ -util_lib/util_make_tree.c: In function 'char* seq2cw_aln_file(char*, char*)': -util_lib/util_make_tree.c:190:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 190 | chdir (dir); - | ~~~~~~^~~~~ -util_lib/util_make_tree.c:192:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 192 | chdir (cdir); - | ~~~~~~~~~^~~~~~ -util_lib/util_make_tree.c: In function 'char* prf_pair2cw_aln_file(char*, char*, char*)': -util_lib/util_make_tree.c:223:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 223 | chdir (dir); - | ~~~~~~^~~~~ -util_lib/util_make_tree.c:226:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 226 | chdir (cdir); - | ~~~~~~~~~^~~~~~ -util_lib/util_make_tree.c: In function 'tnode* seq2fftns1_dnd(Sequence*)': -util_lib/util_make_tree.c:1855:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1855 | chdir (dir); - | ~~~~~~^~~~~ -util_lib/util_make_tree.c:1868:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1868 | chdir (cdir); - | ~~~~~~~~~^~~~~~ -util_lib/util_make_tree.c: In function 'tnode* seq2fftns2_dnd(Sequence*)': -util_lib/util_make_tree.c:1884:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1884 | chdir (dir); - | ~~~~~~^~~~~ -util_lib/util_make_tree.c:1897:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1897 | chdir (cdir); - | ~~~~~~~~~^~~~~~ -util_lib/util_make_tree.c: In function 'tnode* seq2mafft_dnd(Sequence*)': -util_lib/util_make_tree.c:1913:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1913 | chdir (dir); - | ~~~~~~^~~~~ -util_lib/util_make_tree.c:1926:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1926 | chdir (cdir); - | ~~~~~~~~~^~~~~~ -util_lib/util_make_tree.c: In function 'tnode* seq2parttree_dnd(Sequence*)': -util_lib/util_make_tree.c:1943:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1943 | chdir (dir); - | ~~~~~~^~~~~ -util_lib/util_make_tree.c:1956:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1956 | chdir (cdir); - | ~~~~~~~~~^~~~~~ -util_lib/util_make_tree.c: In function 'tnode* seq2dpparttree_dnd(Sequence*)': -util_lib/util_make_tree.c:1973:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1973 | chdir (dir); - | ~~~~~~^~~~~ -util_lib/util_make_tree.c:1988:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1988 | chdir (cdir); - | ~~~~~~~~~^~~~~~ -util_lib/util_make_tree.c: In function 'tnode* seq2fastparttree_dnd(Sequence*)': -util_lib/util_make_tree.c:2006:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2006 | chdir (dir); - | ~~~~~~^~~~~ -util_lib/util_make_tree.c:2019:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2019 | chdir (cdir); - | ~~~~~~~~~^~~~~~ -util_lib/util_make_tree.c: In function 'tnode* seq2cwquick_dnd(Sequence*)': -util_lib/util_make_tree.c:2035:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2035 | chdir (dir); - | ~~~~~~^~~~~ -util_lib/util_make_tree.c:2043:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2043 | chdir (cdir); - | ~~~~~~~~~^~~~~~ -util_lib/util_make_tree.c: In function 'tnode* seq2cw_dnd(Sequence*)': -util_lib/util_make_tree.c:2060:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2060 | chdir (dir); - | ~~~~~~^~~~~ -util_lib/util_make_tree.c:2068:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2068 | chdir (cdir); - | ~~~~~~~~~^~~~~~ -util_lib/util_make_tree.c: In function 'tnode* aln2cw_tree(Alignment*)': -util_lib/util_make_tree.c:2088:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2088 | chdir (dir); - | ~~~~~~^~~~~ -util_lib/util_make_tree.c:2095:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2095 | chdir (cdir); - | ~~~~~~~~~^~~~~~ -util_lib/util_make_tree.c: In function 'tnode* seq2cw_tree(Sequence*)': -util_lib/util_make_tree.c:2110:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2110 | chdir (dir); - | ~~~~~~^~~~~ -util_lib/util_make_tree.c:2119:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2119 | chdir (cdir); - | ~~~~~~~~~^~~~~~ +dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': +dp_lib/util_dp_drivers.c:382:31: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + 382 | sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); + | ^~ +In file included from /usr/include/stdio.h:970, + from dp_lib/util_dp_drivers.c:27: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:382:16: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': +dp_lib/util_dp_drivers.c:373:30: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + 373 | sprintf ( mat, "%s", (strm(m, "default"))?"blosum62mt":m); + | ^~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:373:15: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': +dp_lib/util_dp_drivers.c:386:41: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + 386 | if ( M->matrix[0])sprintf ( mat, "%s", M->matrix); + | ^~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:386:33: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int** read_blast_matrix(char*)': util_lib/reformat.c:14294:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14294 | fscanf ( fp, "%s ", buf); @@ -2036,6 +2059,19 @@ util_lib/reformat.c:14525:19: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 14525 | fgets ( sbuf, VERY_LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +dp_lib/util_dp_drivers.c: In function 'Alignment* realign_block(Alignment*, int, int, char*)': +dp_lib/util_dp_drivers.c:921:25: warning: ' -infile=' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] + 921 | sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); + | ^~~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'Alignment* realign_block(Alignment*, int, int, char*)' at dp_lib/util_dp_drivers.c:921:11: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 38 or more bytes (assuming 1037) into a destination of size 1000 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:548, from t_coffee_lib/t_coffee.c:32: In function 'char* strcpy(char*, const char*)', @@ -2050,19 +2086,6 @@ 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, long unsigned int)' -dp_lib/util_dp_drivers.c: In function 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)': -dp_lib/util_dp_drivers.c:1854:80: warning: '%s' directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] - 1854 | sprintf ( command, "t_coffee -other_pg tc_generic_method.pl -mode=%s -method=%s %s %s%s %s %s%s -tmpdir=%s %s %s", M->executable, M->executable2, M->param1,M->in_flag,infile,M->param2,M->out_flag,outfile,get_tmp_4_tcoffee(),db,M->param); - | ^~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)' at dp_lib/util_dp_drivers.c:1854:11: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 71 or more bytes (assuming 5068) into a destination of size 1000 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'char* make_aln_command(TC_method*, char*, char*)': util_lib/util_constraints_list.c:1286:28: warning: '%s' directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] 1286 | sprintf ( buf, "%s %s %s%s %s %s%s %s", m->executable, m->param1, m->in_flag, seq,m->param2, m->out_flag,aln, m->param); @@ -2078,6 +2101,19 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +dp_lib/util_dp_drivers.c: In function 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)': +dp_lib/util_dp_drivers.c:1854:80: warning: '%s' directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] + 1854 | sprintf ( command, "t_coffee -other_pg tc_generic_method.pl -mode=%s -method=%s %s %s%s %s %s%s -tmpdir=%s %s %s", M->executable, M->executable2, M->param1,M->in_flag,infile,M->param2,M->out_flag,outfile,get_tmp_4_tcoffee(),db,M->param); + | ^~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)' at dp_lib/util_dp_drivers.c:1854:11: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 71 or more bytes (assuming 5068) into a destination of size 1000 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function 'int batch_main(int, char**)': t_coffee_lib/t_coffee.c:5662:66: warning: '%s' directive writing up to 999 bytes into a region of size between 982 and 991 [-Wformat-overflow=] 5662 | sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); @@ -2106,24 +2142,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -io_lib/tree_util.c: In function 'Sequence* get_nexus(char*)': -io_lib/tree_util.c:4597:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] - 4597 | sprintf (index, "%d", i); - | ^~ -io_lib/tree_util.c:4597:39: note: directive argument in the range [1, 2147483647] - 4597 | sprintf (index, "%d", i); - | ^~~~ -In file included from /usr/include/stdio.h:970, - from io_lib/tree_util.c:27: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Sequence* get_nexus(char*)' at io_lib/tree_util.c:4597:17: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 5 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': util_lib/util_constraints_list.c:4922:26: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 4922 | sprintf ( mode, "%s", (CL && in_mode==NULL)?CL->distance_matrix_mode:in_mode); @@ -2150,6 +2168,24 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +io_lib/tree_util.c: In function 'Sequence* get_nexus(char*)': +io_lib/tree_util.c:4597:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] + 4597 | sprintf (index, "%d", i); + | ^~ +io_lib/tree_util.c:4597:39: note: directive argument in the range [1, 2147483647] + 4597 | sprintf (index, "%d", i); + | ^~~~ +In file included from /usr/include/stdio.h:970, + from io_lib/tree_util.c:27: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'Sequence* get_nexus(char*)' at io_lib/tree_util.c:4597:17: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 5 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)': util_lib/util_constraints_list.c:694:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 694 | sprintf ( aln_mode, "%s", method->aln_mode); @@ -2398,9 +2434,9 @@ dh_gencontrol -O--sourcedirectory=t_coffee_source dh_md5sums -O--sourcedirectory=t_coffee_source dh_builddeb -O--sourcedirectory=t_coffee_source -dpkg-deb: building package 't-coffee-examples' in '../t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb'. dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb'. dpkg-deb: building package 't-coffee' in '../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb'. +dpkg-deb: building package 't-coffee-examples' in '../t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2408,12 +2444,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3864704/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3864704/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/2895338 and its subdirectories -I: Current time: Mon Sep 8 07:55:45 -12 2025 -I: pbuilder-time-stamp: 1757361345 +I: removing directory /srv/workspace/pbuilder/3864704 and its subdirectories +I: Current time: Mon Oct 12 16:19:36 +14 2026 +I: pbuilder-time-stamp: 1791771576