Diff of the two buildlogs: -- --- b1/build.log 2025-02-23 15:50:56.974967835 +0000 +++ b2/build.log 2025-02-23 15:53:57.186803128 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Mar 28 10:13:05 -12 2026 -I: pbuilder-time-stamp: 1774735985 +I: Current time: Mon Feb 24 05:51:00 +14 2025 +I: pbuilder-time-stamp: 1740325860 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -34,54 +34,86 @@ 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/90329/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/6279/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 23 15:51 /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/6279/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/6279/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='2aa4061869244713a5262b650e9e9af6' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='90329' - PS1='# ' - PS2='> ' + INVOCATION_ID=f51c5298c1e643c68c8404626a2618d3 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=6279 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.M1PQPyMf/pbuilderrc_8Zek --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.M1PQPyMf/b1 --logfile b1/build.log t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.M1PQPyMf/pbuilderrc_aXrQ --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.M1PQPyMf/b2 --logfile b2/build.log t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos6-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/90329/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/6279/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -147,7 +179,7 @@ Get: 28 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 debhelper all 13.24.1 [920 kB] -Fetched 20.8 MB in 0s (129 MB/s) +Fetched 20.8 MB in 1s (37.2 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 ... 19761 files and directories currently installed.) @@ -282,7 +314,11 @@ 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/6279/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/6279/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 @@ -309,76 +345,40 @@ 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" 'CC=$(CXX)' all - cd t_coffee_source && make -j22 "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" CC=\$\(CXX\) all + cd t_coffee_source && make -j10 "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" 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 -Wformat -Werror=format-security -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 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 +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/evaluate_dirichlet.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 -Wformat -Werror=format-security -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 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 -Wformat -Werror=format-security -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 -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 -Wformat -Werror=format-security -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++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC dp_lib/fsa_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 -Wformat -Werror=format-security -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 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 -Wformat -Werror=format-security -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/pavie_dp.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 -Wformat -Werror=format-security -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++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 -Wformat -Werror=format-security -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++ + CC dp_lib/util_domain_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 -Wformat -Werror=format-security -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++ - 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 - 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 -Wformat -Werror=format-security -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 -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC dp_lib/util_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 -Wformat -Werror=format-security -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 - CC dp_lib/util_dp_est.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 -Wformat -Werror=format-security -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 -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 -Wformat -Werror=format-security -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++ -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 -Wformat -Werror=format-security -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 - CC dp_lib/util_dp_generic_fasta_nw.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC dp_lib/util_dp_gotoh_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 -Wformat -Werror=format-security -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 -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 -Wformat -Werror=format-security -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 -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 -Wformat -Werror=format-security -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 - 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 -Wformat -Werror=format-security -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++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC 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 -Wformat -Werror=format-security -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++ -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++ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_clean_maln.c: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 | ^~~~~~~ @@ -388,27 +388,17 @@ 30 | typedef struct ALNcol | ^~~~~~~ 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/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/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_domain_dp.c: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/evaluate_for_struc.c:34: + 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 | ^~~~~~~ @@ -417,98 +407,56 @@ ./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++]); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 dp_lib/evaluate.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ +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"); + | ~~~~~~^~~~~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_domain_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_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_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_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/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_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_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_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/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_gotoh_nw.c:34: + 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/util_dp_est.c: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 | ^~~~~~~ + 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 -Wformat -Werror=format-security -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 +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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); | ^~~~~~~~~~~~~~~~~~~~~ -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 - | ^~~~~~~ -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; - | ^ -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/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); - | ~~~~~~~^~~~~~~~~~~~~~~ -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.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); @@ -534,37 +482,94 @@ | | | | int double | %3f -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_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 dp_lib/util_dp_ssec_pwaln.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 -Wformat -Werror=format-security -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 +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/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/i386-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/i386-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 ()); + | ~~~~~~~~~~~~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_domain_dp_drivers.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +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); + | ~~~~~~~^~~~~~~~~~~~~~~~~ +dp_lib/evaluate.c:814:26: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 814 | fscanf (fp, "%f %f", &sseq, &mseq); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 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 -Wformat -Werror=format-security -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_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 -Wformat -Werror=format-security -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_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 -Wformat -Werror=format-security -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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC dp_lib/util_graph_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 -Wformat -Werror=format-security -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 +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 ); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC dp_lib/util_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 -Wformat -Werror=format-security -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 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 -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c +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_clean_maln.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ + CC dp_lib/util_dp_est.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 -Wformat -Werror=format-security -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++ - CC fastal/fastal.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 -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c +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 + | ^~~~~~~ + 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 -Wformat -Werror=format-security -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 +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +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; + | ^ + CC 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 -Wformat -Werror=format-security -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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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] @@ -645,74 +650,126 @@ 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)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ~~~~~~~^~~~~~~~~~~~~~~~~ -dp_lib/evaluate.c:814:26: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 814 | fscanf (fp, "%f %f", &sseq, &mseq); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from fastal/diagonal.c:31: + 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_sim.c:32: + 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 | ^~~~~~~ -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); - | ^~ ~~~~~~ +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; + | ^ + CC dp_lib/util_dp_generic_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 -Wformat -Werror=format-security -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++ + CC dp_lib/util_dp_gotoh_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 -Wformat -Werror=format-security -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 +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_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_generic_fasta_nw.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ + CC 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 -Wformat -Werror=format-security -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++ +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 + | ^~~~~~~ + 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 -Wformat -Werror=format-security -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++ +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 + | ^~~~~~~ + CC dp_lib/util_dp_sim.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 -Wformat -Werror=format-security -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++ +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/pavie_dp.c:27: + from dp_lib/util_dp_drivers.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/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 1004) into a destination of size 1000 + inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:382:16: +/usr/include/i386-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/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); - | ^~ ~~~~~~ +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 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)' at dp_lib/pavie_dp.c:1080:15: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 2003 bytes into a destination of size 1000 + inlined from 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)' at dp_lib/util_dp_drivers.c:373:15: +/usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ - 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 -Wformat -Werror=format-security -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 +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/i386-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_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 dp_lib/util_dp_ssec_pwaln.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 -Wformat -Werror=format-security -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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -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); - | ~~~~~^~~~~~~~~~~~~~~~~~~ -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 ); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + | ^~~~~~~ +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/i386-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 ./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 + | ^~~~~~~ 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; @@ -898,60 +955,78 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ + 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 -Wformat -Werror=format-security -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++ + CC dp_lib/util_graph_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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +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/i386-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 ()); + | ~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_suboptimal_nw.c:33: + from fastal/diagonal.c:31: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - 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 -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~ + CC fastal/fastal.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 -Wformat -Werror=format-security -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++ + 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 -Wformat -Werror=format-security -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 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_graph_maln.c: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 | ^~~~~~~ In file included from ./io_lib_header.h:33, - from fastal/fastal.c:34: + 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 | ^~~~~~~ + 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 -Wformat -Werror=format-security -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++ 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 -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/scoring.deps -c -o fastal/scoring.o fastal/scoring.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 -Wformat -Werror=format-security -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++ - 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 -Wformat -Werror=format-security -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 -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC io_lib/tree_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 -Wformat -Werror=format-security -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++ - 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 -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -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_seq_util.c:34: + 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 io_lib/pb_util_read_sequence.c:35: + from fastal/iteration.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ @@ -1011,6 +1086,11 @@ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + | ^~~~~~~ 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); @@ -1031,105 +1111,6 @@ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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; - | ^~~ -io_lib/pb_util_read_seq_util.c: In function 'void* ckvrealloc(void*, size_t)': -io_lib/pb_util_read_seq_util.c:91:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 91 | register void *ret; - | ^~~ -io_lib/pb_util_read_seq_util.c: In function 'char* rtrim(char*)': -io_lib/pb_util_read_seq_util.c:191:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 191 | register int p; - | ^ -io_lib/pb_util_read_seq_util.c: In function 'char* upstr(char*)': -io_lib/pb_util_read_seq_util.c:240:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 240 | register char *s = str; - | ^ -io_lib/pb_util_read_seq_util.c: In function 'char* lowstr(char*)': -io_lib/pb_util_read_seq_util.c:258:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 258 | register char *s = str; - | ^ -io_lib/pb_util_read_seq_util.c: In function 'void get_path(char*, char*)': -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; - | ^ -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 - | ^~~~~~~ -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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~ -io_lib/pb_util_read_seq_util.c: In function 'double getreal(char*, double, double, double)': -io_lib/pb_util_read_seq_util.c:280:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 280 | fgets(line, MAXLINE, stdin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -io_lib/pb_util_read_seq_util.c: In function 'int getint(char*, int, int, int)': -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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -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_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 */ - | ~~~~~^~~~~~~~~~~~~~~~~~~~ -io_lib/pb_util_read_sequence.c:149:51: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 149 | for(i=1;id_name); + | ^~ ~~~~~~~~~ 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/i386-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); - | ^~ + from fastal/scoring.c:28: 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/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + inlined from 'int complete_agreement_score(char*, const char*)' at fastal/scoring.c:624:11: +/usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ -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); - | ^~ +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; + | ^~~ +io_lib/pb_util_read_seq_util.c: In function 'void* ckvrealloc(void*, size_t)': +io_lib/pb_util_read_seq_util.c:91:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 91 | register void *ret; + | ^~~ +io_lib/pb_util_read_seq_util.c: In function 'char* rtrim(char*)': +io_lib/pb_util_read_seq_util.c:191:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 191 | register int p; + | ^ +io_lib/pb_util_read_seq_util.c: In function 'char* upstr(char*)': +io_lib/pb_util_read_seq_util.c:240:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 240 | register char *s = str; + | ^ +io_lib/pb_util_read_seq_util.c: In function 'char* lowstr(char*)': +io_lib/pb_util_read_seq_util.c:258:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 258 | register char *s = str; + | ^ +io_lib/pb_util_read_seq_util.c: In function 'void get_path(char*, char*)': +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_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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~ +io_lib/pb_util_read_seq_util.c: In function 'double getreal(char*, double, double, double)': +io_lib/pb_util_read_seq_util.c:280:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 280 | fgets(line, MAXLINE, stdin); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +io_lib/pb_util_read_seq_util.c: In function 'int getint(char*, int, int, int)': +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ + 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 -Wformat -Werror=format-security -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++ +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 + | ^~~~~~~ + CC io_lib/tree_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 -Wformat -Werror=format-security -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++ +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_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 */ + | ~~~~~^~~~~~~~~~~~~~~~~~~~ +io_lib/pb_util_read_sequence.c:149:51: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 149 | for(i=1;idp_mode); + | ^~ 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: + inlined from 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)' at dp_lib/util_dp_drivers.c:3717:13: /usr/include/i386-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, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1316,9 +1382,18 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - 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 -Wformat -Werror=format-security -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++ +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); + | ^~~~~~~~~~~~~~~~~~~~~ +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 | } + | ^ +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 | } + | ^ 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 | } @@ -1343,6 +1418,9 @@ io_lib/tree_util.c:7204:1: warning: no return statement in function returning non-void [-Wreturn-type] 7204 | } | ^ + 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 -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.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) @@ -1360,27 +1438,8 @@ io_lib/tree_util.c:9947:46: note: declared here 9947 | void wn_c (unsigned long n, unsigned long t); | ~~~~~~~~~~~~~~^ - 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 -Wformat -Werror=format-security -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++ -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/i386-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 ()); - | ~~~~~~~~~~~~~~~~~ - 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 -Wformat -Werror=format-security -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 -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 -Wformat -Werror=format-security -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 + 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 -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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] @@ -1389,15 +1448,50 @@ 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ +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 | } + | ^ + 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 -Wformat -Werror=format-security -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++ + 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 -Wformat -Werror=format-security -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 +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +km_coffee/km_util.c: In function 'void* my_malloc(size_t)': +km_coffee/km_util.c:49:76: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + 49 | fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size); + | ~~^ ~~~~ + | | | + | | size_t {aka unsigned int} + | long int + | %i +km_coffee/km_util.c: In function 'void* my_calloc(size_t, size_t)': +km_coffee/km_util.c:61:76: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + 61 | fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size*num); + | ~~^ ~~~~~~~~ + | | | + | long int size_t {aka unsigned int} + | %i +km_coffee/km_util.c: In function 'void* my_realloc(void*, size_t)': +km_coffee/km_util.c:74:76: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] + 74 | fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size); + | ~~^ ~~~~ + | | | + | | size_t {aka unsigned int} + | long int + | %i +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* 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 | ^~~~~~~ -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 | } - | ^ km_coffee/km_coffee.c: In function 'void traverse_km_tree(KM_node*, int*, const SeqSet*, char*, int, int, int, char*)': km_coffee/km_coffee.c:148:53: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 148 | sprintf(command, "%li",current->id); @@ -1429,10 +1523,7 @@ | | | | long int size_t {aka unsigned int} | %i -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); - | ^~ ~~~~~~~~~ + CC km_coffee/kmeans.c km_coffee/km_coffee.c:172:73: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 172 | sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %li.fa -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, gapopen, gapext, method); | ~~^ ~~~~~~~~~~~ @@ -1445,23 +1536,13 @@ | | | | long int size_t {aka unsigned int} | %i -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/i386-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_coffee.c:174:73: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 174 | sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %s -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null ", current->id, out_f, n_cores, gapopen, gapext, method); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i +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 -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/kmeans.deps -c -o km_coffee/kmeans.o km_coffee/kmeans.c km_coffee/km_coffee.c:185:53: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 185 | sprintf(command, "%li.fa",current->id); | ~~^ ~~~~~~~~~~~ @@ -1480,58 +1561,25 @@ | | | | long int size_t {aka unsigned int} | %i -km_coffee/km_util.c: In function 'void* my_malloc(size_t)': -km_coffee/km_util.c:49:76: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 49 | fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size); - | ~~^ ~~~~ - | | | - | | size_t {aka unsigned int} - | long int - | %i -km_coffee/km_util.c: In function 'void* my_calloc(size_t, size_t)': -km_coffee/km_util.c:61:76: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 61 | fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size*num); - | ~~^ ~~~~~~~~ - | | | - | long int size_t {aka unsigned int} - | %i -km_coffee/km_util.c: In function 'void* my_realloc(void*, size_t)': -km_coffee/km_util.c:74:76: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] - 74 | fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size); - | ~~^ ~~~~ - | | | - | | size_t {aka unsigned int} - | long int - | %i -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/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 -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 -Wformat -Werror=format-security -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++ 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); | ~~~~~^~~~~~~~~~~~ -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/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 -Wformat -Werror=format-security -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 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 -Wformat -Werror=format-security -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++ - 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 -Wformat -Werror=format-security -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 + 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 -Wformat -Werror=format-security -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 +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 -Wformat -Werror=format-security -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++ + 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 -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.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: + 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 | ^~~~~~~ @@ -1544,7 +1592,7 @@ 7172 | else { w=seq2dpa_weight (S, "longuest");fprintf ( le, "default longuest\n", dpa_weight);} | ^~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from util_lib/aln_convertion_util.c: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 | ^~~~~~~ @@ -1556,43 +1604,33 @@ t_coffee_lib/t_coffee.c:6816:1: warning: control reaches end of non-void function [-Wreturn-type] 6816 | } | ^ - 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 -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util.deps -c -o util_lib/util.o util_lib/util.c +In file included from ./io_lib_header.h:33, + 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 + | ^~~~~~~ + 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 -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/random.deps -c -o util_lib/random.o util_lib/random.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 -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat.deps -c -o util_lib/reformat.o util_lib/reformat.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 -Wformat -Werror=format-security -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++ -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)) - | ^~~~ + 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 -Wformat -Werror=format-security -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++ In file included from ./io_lib_header.h: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 | ^~~~~~~ +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/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 | } | ^ -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/i386-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 ()); - | ~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/reformat.c:35: -./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 | } @@ -1602,18 +1640,25 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -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 - | ^~~~~~~~ - 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 -Wformat -Werror=format-security -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 -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/util_aln_analyze.c:33: + from util_lib/reformat.c:35: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ +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* 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/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" ); @@ -1633,54 +1678,27 @@ util_lib/reformat_struc.c:416:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 416 | fscanf (fp, "%*s %s %s %*c %d %f %f %f\n",A->type, A->res,&A->res_num, &A->x, &A->y, &A->z); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h: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_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/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 cherry(int, char**)': -util_lib/util.c:1009:1: warning: no return statement in function returning non-void [-Wreturn-type] - 1009 | } - | ^ -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/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 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/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_analyse_constraints_list.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ +In file included from /usr/include/string.h:548, + from t_coffee_lib/t_coffee.c:32: +In function 'char* strcpy(char*, const char*)', + inlined from 'char** km_coffee(int, char**)' at t_coffee_lib/t_coffee.c:6543:14: +/usr/include/i386-linux-gnu/bits/string_fortified.h:81:33: warning: argument 1 null where non-null expected [-Wnonnull] + 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/i386-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, unsigned int)' +In function 'char* strcpy(char*, const char*)', + inlined from 'char** km_coffee(int, char**)' at t_coffee_lib/t_coffee.c:6545:14: +/usr/include/i386-linux-gnu/bits/string_fortified.h:81:33: warning: argument 1 null where non-null expected [-Wnonnull] + 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/i386-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, unsigned int)' + 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 -Wformat -Werror=format-security -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++ 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 | } @@ -1689,8 +1707,6 @@ util_lib/reformat.c:1332:1: warning: control reaches end of non-void function [-Wreturn-type] 1332 | } | ^ - 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 -Wformat -Werror=format-security -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 util_lib/reformat.c: In function 'Alignment* quick_read_aln_static(char*)': util_lib/reformat.c:1371:1: warning: control reaches end of non-void function [-Wreturn-type] 1371 | } @@ -1737,7 +1753,6 @@ 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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); @@ -1750,47 +1765,6 @@ util_lib/reformat.c:2507:1: warning: control reaches end of non-void function [-Wreturn-type] 2507 | } | ^ -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]*/ - | ~~~~~^~~~~~~~~~~~~~~~~~~~ -util_lib/util.c:286:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 286 | fread( rra, size, len,fp); /*rra=ra[ir]*/ - | ~~~~~^~~~~~~~~~~~~~~~~~~~ -util_lib/util.c:289:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 289 | fread( rrb, size, len,fp); /*rrb=ra[0]*/ - | ~~~~~^~~~~~~~~~~~~~~~~~~~ -util_lib/util.c:306:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 306 | fread (ra_j, size, len, fp); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c:311:25: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 311 | fread (ra_j_1, size, len, fp); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'void* bsearch_file(const void*, int*, int, int, FILE*, int, int, size_t, int (*)(const void*, const void*, int, int, size_t))': -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); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'int** input_array_int(char*)': -util_lib/util.c:1805:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1805 | fscanf (fp, "%d\n", &len); - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -util_lib/util.c:1809:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1809 | fscanf(fp, "%d ", &len2); - | ~~~~~~^~~~~~~~~~~~~~~~~~ -util_lib/util.c:1812:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1812 | fscanf(fp, "%d ", &array[a][b]); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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/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); @@ -1831,13 +1805,10 @@ util_lib/reformat.c:4549:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4549 | fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ - 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 -Wformat -Werror=format-security -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 util_lib/reformat.c: In function 'Sequence* get_dialign_sequence(char*)': util_lib/reformat.c:4624:33: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4624 | {fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/reformat.c: In function 'int get_next_fasta_sequence(FILE*, char**, char**, char**)': 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); @@ -1850,10 +1821,6 @@ util_lib/reformat.c:6077:25: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 6077 | {fscanf (fp, "%*d >%s", name[nseq++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ~~~~~~~^~~~~~~~~~~~~~ util_lib/reformat.c: In function 'Alignment* read_gotoh_aln(char*, Alignment*)': util_lib/reformat.c:6126:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6126 | fgets(buf, VERY_LONG_STRING, fp); @@ -1869,10 +1836,9 @@ 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.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); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 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 -Wformat -Werror=format-security -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++ 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); @@ -1883,10 +1849,6 @@ util_lib/reformat.c:14332:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14332 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ -util_lib/util.c: In function 'char* count_strings_in_file(char*, char*)': -util_lib/util.c:5761:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 5761 | fscanf (fp, "%s\n",list[n]); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int** read_blast_matrix_old(char*)': util_lib/reformat.c:14357:19: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 14357 | fgets ( sbuf, VERY_LONG_STRING, fp); @@ -1904,8 +1866,116 @@ 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 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 -Wformat -Werror=format-security -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 +In file included from ./io_lib_header.h: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 + | ^~~~~~~ + 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 -Wformat -Werror=format-security -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 +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/util_aln_analyze.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 | } + | ^ +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/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 | } + | ^ +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 | } + | ^ +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); + | ^~ ~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:970, + from t_coffee_lib/t_coffee.c:27: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int batch_main(int, char**)' at t_coffee_lib/t_coffee.c:5662:18: +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1018) 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 ./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 + | ^~~~~~~ +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]*/ + | ~~~~~^~~~~~~~~~~~~~~~~~~~ +util_lib/util.c:286:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 286 | fread( rra, size, len,fp); /*rra=ra[ir]*/ + | ~~~~~^~~~~~~~~~~~~~~~~~~~ +util_lib/util.c:289:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 289 | fread( rrb, size, len,fp); /*rrb=ra[0]*/ + | ~~~~~^~~~~~~~~~~~~~~~~~~~ +util_lib/util.c:306:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 306 | fread (ra_j, size, len, fp); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c:311:25: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 311 | fread (ra_j_1, size, len, fp); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'void* bsearch_file(const void*, int*, int, int, FILE*, int, int, size_t, int (*)(const void*, const void*, int, int, size_t))': +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); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'int** input_array_int(char*)': +util_lib/util.c:1805:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1805 | fscanf (fp, "%d\n", &len); + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +util_lib/util.c:1809:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1809 | fscanf(fp, "%d ", &len2); + | ~~~~~~^~~~~~~~~~~~~~~~~~ +util_lib/util.c:1812:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1812 | fscanf(fp, "%d ", &array[a][b]); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +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.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); + | ~~~~~~~^~~~~~~~~~~~~~ +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); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'char* count_strings_in_file(char*, char*)': +util_lib/util.c:5761:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 5761 | fscanf (fp, "%s\n",list[n]); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* redirect_stderr(char*)': util_lib/util.c:6301:12: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6301 | freopen(stderr_file, "w", stderr); @@ -1914,7 +1984,6 @@ util_lib/util.c:6344:12: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6344 | freopen(stdout_file, "w", stdout); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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); @@ -1942,29 +2011,15 @@ util_lib/util.c:8528:10: warning: control reaches end of non-void function [-Wreturn-type] 8528 | myexit (EXIT_FAILURE); | ~~~~~~~^~~~~~~~~~~~~~ + 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 -Wformat -Werror=format-security -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 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 | } | ^ - 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 -Wformat -Werror=format-security -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 cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -In file included from /usr/include/string.h:548, - from t_coffee_lib/t_coffee.c:32: -In function 'char* strcpy(char*, const char*)', - inlined from 'char** km_coffee(int, char**)' at t_coffee_lib/t_coffee.c:6543:14: -/usr/include/i386-linux-gnu/bits/string_fortified.h:81:33: warning: argument 1 null where non-null expected [-Wnonnull] - 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/i386-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, unsigned int)' -In function 'char* strcpy(char*, const char*)', - inlined from 'char** km_coffee(int, char**)' at t_coffee_lib/t_coffee.c:6545:14: -/usr/include/i386-linux-gnu/bits/string_fortified.h:81:33: warning: argument 1 null where non-null expected [-Wnonnull] - 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/i386-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, unsigned int)' - 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 -Wformat -Werror=format-security -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 + 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 -Wformat -Werror=format-security -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++ In file included from ./io_lib_header.h:33, from util_lib/util_constraints_list.c:37: @@ -1976,8 +2031,8 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - 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 -Wformat -Werror=format-security -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 + 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 -Wformat -Werror=format-security -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++ 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] @@ -1987,20 +2042,28 @@ util_lib/util_constraints_list.c:2224:49: warning: too many arguments for format [-Wformat-extra-args] 2224 | fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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_constraints_list.c: In function 'Constraint_list* read_constraint_list_file(Constraint_list*, char*)': 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); | ^~~~~~~~~~~~~~~~~~~ -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 - | ^~~~~~~ +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/i386-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* 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); @@ -2033,15 +2096,34 @@ util_lib/util_constraints_list.c:2979:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2979 | fgets (line , 200 , fp); | ~~~~~~^~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c: In function 'Constraint_list* nfork_relax_constraint_list_4gp(Constraint_list*)': +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]); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + | ^~~~~~~ + 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 -Wformat -Werror=format-security -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 +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/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_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 -Wformat -Werror=format-security -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++ + 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 -Wformat -Werror=format-security -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 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_constraints_list.c: In function 'Constraint_list* nfork_relax_constraint_list_4gp(Constraint_list*)': -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]); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 @@ -2153,21 +2235,6 @@ 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); | ~~~~~~~~~^~~~~~ -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); - | ^~ ~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from t_coffee_lib/t_coffee.c:27: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'int batch_main(int, char**)' at t_coffee_lib/t_coffee.c:5662:18: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1018) 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); @@ -2183,12 +2250,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -dp_lib/util_dp_drivers.c: In function 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)': -dp_lib/util_dp_drivers.c:3717:25: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - 3717 | sprintf ( dp_mode, "%s", CL->dp_mode); - | ^~ +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); + | ^~ In function 'int sprintf(char*, const char*, ...)', - inlined from 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)' at dp_lib/util_dp_drivers.c:3717:13: + inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4922:10: /usr/include/i386-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, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2196,44 +2263,42 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: +util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': +util_lib/util_constraints_list.c:4923:30: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + 4923 | sprintf ( sim_mode, "%s", (CL && in_sim_mode==NULL)?CL->distance_matrix_sim_mode:in_sim_mode); + | ^~ In function 'int sprintf(char*, const char*, ...)', - inlined from 'Sequence* get_nexus(char*)' at io_lib/tree_util.c:4597:17: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 5 + inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4923:10: +/usr/include/i386-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/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); - | ^~ +util_lib/util.c: In function 'char* get_cache_4_tcoffee()': +util_lib/util.c:5385:42: warning: '/cache/' directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] + 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); + | ^~~~~~~ +In file included from /usr/include/stdio.h:970, + from util_lib/util.c:32: In function 'int sprintf(char*, const char*, ...)', - inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4922:10: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + inlined from 'char* get_cache_4_tcoffee()' at util_lib/util.c:5385:20: +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 8 and 1007 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 ()); | ~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': -util_lib/util_constraints_list.c:4923:30: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - 4923 | sprintf ( sim_mode, "%s", (CL && in_sim_mode==NULL)?CL->distance_matrix_sim_mode:in_sim_mode); - | ^~ +util_lib/util.c: In function 'char* get_plugins_4_tcoffee()': +util_lib/util.c:5435:43: warning: '/plugins/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] + 5435 | else sprintf (plugins_4_tcoffee, "%s/plugins/%s/", get_dir_4_tcoffee(), get_os()); + | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', - inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4923:10: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + inlined from 'char* get_plugins_4_tcoffee()' at util_lib/util.c:5435:20, + inlined from 'char* get_plugins_4_tcoffee()' at util_lib/util.c:5419:7: +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 11 and 1109 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, @@ -2292,35 +2357,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'char* get_cache_4_tcoffee()': -util_lib/util.c:5385:42: warning: '/cache/' directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] - 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); - | ^~~~~~~ -In file included from /usr/include/stdio.h:970, - from util_lib/util.c:32: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'char* get_cache_4_tcoffee()' at util_lib/util.c:5385:20: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 8 and 1007 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 ()); - | ~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'char* get_plugins_4_tcoffee()': -util_lib/util.c:5435:43: warning: '/plugins/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] - 5435 | else sprintf (plugins_4_tcoffee, "%s/plugins/%s/", get_dir_4_tcoffee(), get_os()); - | ^~~~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'char* get_plugins_4_tcoffee()' at util_lib/util.c:5435:20, - inlined from 'char* get_plugins_4_tcoffee()' at util_lib/util.c:5419:7: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 11 and 1109 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 ()); - | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_mcoffee_4_tcoffee()': util_lib/util.c:5400:44: warning: '/mcoffee/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); @@ -2391,10 +2427,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'FILE* display_output_filename(FILE*, char*, char*, char*, int)': -util_lib/util.c:8658:68: warning: '%s' directive argument is null [-Wformat-overflow=] - 8658 | fprintf ( io, "\n\t#### File Type= %-15s Format= %-15s Name= %s",type, format, name ); - | ^~ util_lib/reformat.c: In function 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)': util_lib/reformat.c:13639:34: warning: ' -method ' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 13639 | sprintf ( command, "%s -method %s -aln %s -tree %s -dmatrix %s -weightfile %s %s",method_4_msa_weights, action_list[1],aln_name, tree_name, dist_matrix_name,weight_name, TO_NULL_DEVICE); @@ -2414,6 +2446,10 @@ util_lib/reformat.c:11638:32: warning: '%s' directive argument is null [-Wformat-overflow=] 11638 | sprintf (type, "%s", ACTION (2)); | ^~ +util_lib/util.c: In function 'FILE* display_output_filename(FILE*, char*, char*, char*, int)': +util_lib/util.c:8658:68: warning: '%s' directive argument is null [-Wformat-overflow=] + 8658 | fprintf ( io, "\n\t#### File Type= %-15s Format= %-15s Name= %s",type, format, name ); + | ^~ util_lib/util.c: In function 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)': util_lib/util.c:5400:44: warning: '/mcoffee/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); @@ -2488,9 +2524,9 @@ 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_i386.deb'. dpkg-deb: building package 't-coffee' in '../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_i386.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_i386.buildinfo dpkg-genchanges --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2498,12 +2534,14 @@ 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/6279/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/6279/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/90329 and its subdirectories -I: Current time: Sat Mar 28 10:13:56 -12 2026 -I: pbuilder-time-stamp: 1774736036 +I: removing directory /srv/workspace/pbuilder/6279 and its subdirectories +I: Current time: Mon Feb 24 05:53:56 +14 2025 +I: pbuilder-time-stamp: 1740326036