Diff of the two buildlogs: -- --- b1/build.log 2025-02-22 08:56:54.305142913 +0000 +++ b2/build.log 2025-02-22 08:58:24.869060022 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Mar 27 03:18:26 -12 2026 -I: pbuilder-time-stamp: 1774624706 +I: Current time: Sat Feb 22 22:56:56 +14 2025 +I: pbuilder-time-stamp: 1740214616 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -33,51 +33,83 @@ 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/1959640/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 22 08:57 /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/2436871/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + 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]="x86_64-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=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='2d953a6b81f74606aef918c2eabdbc3e' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1959640' - PS1='# ' - PS2='> ' + INVOCATION_ID=b18f828c2ef5414f8a5731eba72e37b8 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2436871 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.2k9gWSUH/pbuilderrc_Jcqt --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b1 --logfile b1/build.log t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.2k9gWSUH/pbuilderrc_zEXm --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2k9gWSUH/b2 --logfile b2/build.log t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-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/1959640/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2436871/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -143,7 +175,7 @@ Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] -Fetched 20.6 MB in 2s (11.4 MB/s) +Fetched 20.6 MB in 1s (18.0 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19858 files and directories currently installed.) @@ -278,7 +310,11 @@ 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/2436871/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2436871/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 @@ -310,114 +346,64 @@ CC dev_lib/dev1.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dev_lib/dev1.deps -c -o dev_lib/dev1.o dev_lib/dev1.c CC dp_lib/CUSTOM_evaluate_for_struc.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/evaluate.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c CC dp_lib/evaluate_dirichlet.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c + CC dp_lib/evaluate_for_domain.c + CC dp_lib/evaluate_for_struc.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC dp_lib/pavie_dp.c CC dp_lib/fsa_dp.c - CC dp_lib/showpair.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/showpair.deps -c -o dp_lib/showpair.o dp_lib/showpair.c - CC dp_lib/util_dp_cdna_fasta_nw.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o dp_lib/util_domain_dp.c - CC dp_lib/evaluate_for_domain.c - CC dp_lib/util_domain_dp_drivers.c + CC 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++ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp_drivers.deps -c -o dp_lib/util_domain_dp_drivers.o dp_lib/util_domain_dp_drivers.c + CC dp_lib/showpair.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/showpair.deps -c -o dp_lib/showpair.o dp_lib/showpair.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_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++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC dp_lib/util_domain_dp.c + CC dp_lib/util_domain_dp_drivers.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp_drivers.deps -c -o dp_lib/util_domain_dp_drivers.o dp_lib/util_domain_dp_drivers.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC dp_lib/util_dp_cdna_fasta_nw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_cdna_fasta_nw.deps -c -o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_cdna_fasta_nw.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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/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_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 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/CUSTOM_evaluate_for_struc.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -dev_lib/dev1.c: In function 'void aln2hitMat(Alignment*, char*)': -dev_lib/dev1.c:89:26: warning: too many arguments for format [-Wformat-extra-args] - 89 | fprintf (stdout, "Process positions\n", i); - | ^~~~~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/fsa_dp.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/util_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/evaluate_dirichlet.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_clean_maln.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_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++ In file included from ./io_lib_header.h:33, from dp_lib/evaluate_for_struc.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_domain_dp.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, from dp_lib/evaluate.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/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/pavie_dp.c:33: + from dp_lib/fsa_dp.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_clean_maln.c:33: + from dev_lib/dev1.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_drivers.deps -c -o dp_lib/util_dp_drivers.o dp_lib/util_dp_drivers.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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); @@ -431,6 +417,15 @@ 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/pavie_dp.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +dev_lib/dev1.c: In function 'void aln2hitMat(Alignment*, char*)': +dev_lib/dev1.c:89:26: warning: too many arguments for format [-Wformat-extra-args] + 89 | fprintf (stdout, "Process positions\n", i); + | ^~~~~~~~~~~~~~~~~~~~~ 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); @@ -456,6 +451,26 @@ | | | | int double | %3f +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/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_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_cdna_fasta_nw.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 '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++]); @@ -471,12 +486,6 @@ 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); | ~~~~~~~^~~~~~~~~~~~~~~ - 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_est.deps -c -o dp_lib/util_dp_est.o dp_lib/util_dp_est.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC dp_lib/util_dp_fasta_nw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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); @@ -487,25 +496,23 @@ 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_fasta_sw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_drivers.c: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_domain_dp.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c + CC dp_lib/util_dp_clean_maln.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_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++ -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/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); @@ -535,15 +542,36 @@ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_generic_fasta_nw.c:34: + 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_drivers.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_drivers.deps -c -o dp_lib/util_dp_drivers.o dp_lib/util_dp_drivers.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC dp_lib/util_dp_est.c + CC dp_lib/util_dp_fasta_nw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC dp_lib/util_dp_fasta_sw.c + 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_nw.deps -c -o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_nw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC dp_lib/util_dp_mm_nw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c +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_fasta_nw.c:34: + 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 | ^~~~~~~ @@ -552,10 +580,34 @@ ./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_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_generic_fasta_nw.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from 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 + | ^~~~~~~ +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/util_dp_fasta_nw.c: In function 'int* makepointtable(int*, int*, int)': dp_lib/util_dp_fasta_nw.c:157:17: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 157 | register int *p; | ^ +In file included from ./io_lib_header.h:33, + from 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 + | ^~~~~~~ dp_lib/util_dp_drivers.c: In function 'char* seq_file2msa_file(char*, char*, char*)': dp_lib/util_dp_drivers.c:1014:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1014 | chdir (dir); @@ -618,8 +670,6 @@ dp_lib/util_dp_drivers.c:1981:15: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1981 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c dp_lib/util_dp_drivers.c: In function 'Constraint_list* sap_pair(char*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:2073:17: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2073 | atoi(strtok (seq,SEPARATORS)); @@ -637,45 +687,52 @@ 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)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC dp_lib/util_dp_mm_nw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c -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: + 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 | ^~~~~~~ +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_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_sim.deps -c -o dp_lib/util_dp_sim.o dp_lib/util_dp_sim.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_ssec_pwaln.deps -c -o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_ssec_pwaln.c 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_suboptimal_nw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c +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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c +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: + from dp_lib/util_dp_ssec_pwaln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_gotoh_sw.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 | ^~~~~~~ - CC dp_lib/util_dp_suboptimal_nw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c -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_sim.c:32: + from dp_lib/util_graph_maln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -dp_lib/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 fastal/diagonal.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.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_mm_nw.c: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 | ^~~~~~~ @@ -692,6 +749,11 @@ | ^~ | -- dp_lib/util_dp_sim.c:248:20: note: or replace parentheses with braces to value-initialize a variable +In file included from ./io_lib_header.h:33, + from fastal/diagonal.c:31: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ dp_lib/util_dp_sim.c: In function 'int big_pass(int*, int*, int, int, int, int)': dp_lib/util_dp_sim.c:481:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 481 | { register int i, j; /* row and column indices */ @@ -859,16 +921,6 @@ dp_lib/util_dp_sim.c:912:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_ssec_pwaln.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_suboptimal_nw.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ dp_lib/util_dp_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); @@ -910,9 +962,21 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c -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); + | ~~~~~^~~~~~~~~~~~~~~~~~~ + 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c 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); @@ -926,38 +990,20 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - CC fastal/diagonal.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -In file included from ./io_lib_header.h: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/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c + CC fastal/fastal_opt_parsing.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal_opt_parsing.deps -c -o fastal/fastal_opt_parsing.o fastal/fastal_opt_parsing.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC fastal/iteration.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -fastal/diagonal.c: In function 'int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)': -fastal/diagonal.c:434:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 434 | system(blast_command); - | ~~~~~~^~~~~~~~~~~~~~~ -fastal/diagonal.c:439:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 439 | fgets(line, 300, diag_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/diagonal.c:440:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 440 | fgets(line, 300, diag_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/diagonal.c:441:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 441 | fgets(line, 300, diag_f); - | ~~~~~^~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_graph_maln.c:33: + from fastal/fastal.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC fastal/fastal_opt_parsing.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal_opt_parsing.deps -c -o fastal/fastal_opt_parsing.o fastal/fastal_opt_parsing.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC fastal/parttree.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.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); @@ -971,16 +1017,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - CC fastal/iteration.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -In file included from ./io_lib_header.h:33, - from fastal/fastal.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ - CC fastal/parttree.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/scoring.deps -c -o fastal/scoring.o fastal/scoring.c @@ -1061,17 +1097,14 @@ fastal/fastal.c:3643:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3643 | fgets(aligned_sequence, alignment_length+3, edit_seq_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC fastal/tree.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/tree.deps -c -o fastal/tree.o fastal/tree.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, from fastal/iteration.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC fastal/tree.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/tree.deps -c -o fastal/tree.o fastal/tree.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC io_lib/io_func.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/io_func.deps -c -o io_lib/io_func.o io_lib/io_func.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/iteration.c: In function 'void split_set(FILE*, Fastal_profile*, Fastal_profile*, char*, int, int*, char*)': fastal/iteration.c:185:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 185 | fgets(line, LINE_LENGTH , alignment_file); @@ -1116,20 +1149,12 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC io_lib/pb_util_read_seq_util.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/parttree.c: In function 'void makepointtable_fast(int*, int, int, int)': fastal/parttree.c:757:23: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 757 | register int *p; | ^ In file included from ./io_lib_header.h:33, - from 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/tree.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ @@ -1143,30 +1168,6 @@ fastal/scoring.c:82:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 82 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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; - | ^ fastal/scoring.c: In function 'void compute_ref_alignments(char*, char*, int, int)': fastal/scoring.c:384:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 384 | fgets(line, LINE_LENGTH, seq_file); @@ -1181,10 +1182,6 @@ fastal/scoring.c:502:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 502 | system(command); | ~~~~~~^~~~~~~~~ -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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function 'double agreement_score(char*, char*)': fastal/scoring.c:583:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 583 | fgets(line, LINE_LENGTH, result); @@ -1195,19 +1192,6 @@ fastal/scoring.c:585:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 585 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from fastal/tree.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ fastal/parttree.c: In function 'int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)': fastal/parttree.c:695:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 695 | fgets(line, 500, aln_f); @@ -1242,30 +1226,10 @@ fastal/parttree.c:962:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 962 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -io_lib/io_func.c: In function 'int output_raw_score(Alignment*, Alignment*, char*)': -io_lib/io_func.c:1235:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null] - 1235 | if (!A)return NULL; - | ^~~~ -io_lib/io_func.c: In function 'int aln2compressed_ps(Alignment*, char*)': -io_lib/io_func.c:2076:1: warning: no return statement in function returning non-void [-Wreturn-type] - 2076 | } - | ^ -io_lib/io_func.c: In function 'int** read_matrice(char*)': -io_lib/io_func.c:511:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 511 | fscanf ( fp, "\n"); - | ~~~~~~~^~~~~~~~~~~ -io_lib/io_func.c: In function 'void get_rgb_values(int, Color*)': -io_lib/io_func.c:971:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 971 | fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC io_lib/pb_util_read_sequence.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/tree_util.deps -c -o io_lib/tree_util.o io_lib/tree_util.c - CC km_coffee/Stack.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC io_lib/io_func.c + CC io_lib/pb_util_read_seq_util.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/io_func.deps -c -o io_lib/io_func.o io_lib/io_func.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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=] @@ -1282,17 +1246,82 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - CC km_coffee/Vector.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c 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: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ + CC io_lib/pb_util_read_sequence.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +io_lib/io_func.c: In function 'int output_raw_score(Alignment*, Alignment*, char*)': +io_lib/io_func.c:1235:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null] + 1235 | if (!A)return NULL; + | ^~~~ +io_lib/io_func.c: In function 'int aln2compressed_ps(Alignment*, char*)': +io_lib/io_func.c:2076:1: warning: no return statement in function returning non-void [-Wreturn-type] + 2076 | } + | ^ +io_lib/io_func.c: In function 'int** read_matrice(char*)': +io_lib/io_func.c:511:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 511 | fscanf ( fp, "\n"); + | ~~~~~~~^~~~~~~~~~~ +io_lib/io_func.c: In function 'void get_rgb_values(int, Color*)': +io_lib/io_func.c:971:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 971 | fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 km_coffee/classes.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c + CC 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/tree_util.deps -c -o io_lib/tree_util.o io_lib/tree_util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC km_coffee/Stack.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c 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; @@ -1330,6 +1359,10 @@ io_lib/pb_util_read_sequence.c:280:46: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 280 | fgets(line,MAXLINE+1,fin); | ~~~~~^~~~~~~~~~~~~~~~~~~~ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC km_coffee/Vector.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c +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/tree_util.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -1399,6 +1432,15 @@ io_lib/tree_util.c:9772:1: warning: control reaches end of non-void function [-Wreturn-type] 9772 | } | ^ + CC km_coffee/classes.c + CC km_coffee/km_coffee.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_coffee.deps -c -o km_coffee/km_coffee.o km_coffee/km_coffee.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC km_coffee/km_util.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_util.deps -c -o km_coffee/km_util.o km_coffee/km_util.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ km_coffee/Vector.c: In function 'void print_vecs(VectorSet*, char*)': km_coffee/Vector.c:869:34: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 869 | fprintf(out_F, "%i ", i); @@ -1406,26 +1448,6 @@ | | | | int size_t {aka long unsigned int} | %li - CC km_coffee/km_coffee.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_coffee.deps -c -o km_coffee/km_coffee.o km_coffee/km_coffee.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC km_coffee/km_util.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_util.deps -c -o km_coffee/km_util.o km_coffee/km_util.c - CC km_coffee/kmeans.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/kmeans.deps -c -o km_coffee/kmeans.o km_coffee/kmeans.c -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++ -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 - | ^~~~~~~ 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); @@ -1439,24 +1461,43 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - CC t_coffee_lib/t_coffee.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF t_coffee_lib/t_coffee.deps -c -o t_coffee_lib/t_coffee.o t_coffee_lib/t_coffee.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +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 + | ^~~~~~~ +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* 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); | ~~~~~^~~~~~~~~~~~ + CC km_coffee/kmeans.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/kmeans.deps -c -o km_coffee/kmeans.o km_coffee/kmeans.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC t_coffee_lib/t_coffee.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF t_coffee_lib/t_coffee.deps -c -o t_coffee_lib/t_coffee.o t_coffee_lib/t_coffee.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_compare.deps -c -o util_lib/aln_compare.o util_lib/aln_compare.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC util_lib/aln_convertion_util.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_convertion_util.deps -c -o util_lib/aln_convertion_util.o util_lib/aln_convertion_util.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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/aln_convertion_util.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_convertion_util.deps -c -o util_lib/aln_convertion_util.o util_lib/aln_convertion_util.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +In file included from ./io_lib_header.h:33, + from util_lib/aln_compare.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ t_coffee_lib/t_coffee.c: In function 'char** km_coffee(int, char**)': t_coffee_lib/t_coffee.c:6577:1: warning: no return statement in function returning non-void [-Wreturn-type] 6577 | } @@ -1465,11 +1506,8 @@ t_coffee_lib/t_coffee.c:7172:57: warning: too many arguments for format [-Wformat-extra-args] 7172 | else { w=seq2dpa_weight (S, "longuest");fprintf ( le, "default longuest\n", dpa_weight);} | ^~~~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/aln_compare.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ + CC util_lib/hsearch.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c t_coffee_lib/t_coffee.c: In function 'int run_other_pg(int, char**)': t_coffee_lib/t_coffee.c:6139:30: warning: control reaches end of non-void function [-Wreturn-type] 6139 | unpack_all_perl_script (argv[0]+strlen ("unpack_")); @@ -1478,23 +1516,15 @@ t_coffee_lib/t_coffee.c:6816:1: warning: control reaches end of non-void function [-Wreturn-type] 6816 | } | ^ - CC util_lib/hsearch.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/random.deps -c -o util_lib/random.o util_lib/random.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC util_lib/reformat.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat.deps -c -o util_lib/reformat.o util_lib/reformat.c +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_convertion_util.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC util_lib/reformat_struc.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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)) @@ -1512,16 +1542,11 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/reformat.c:35: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/reformat_struc.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ + CC util_lib/reformat.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat.deps -c -o util_lib/reformat.o util_lib/reformat.c +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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c 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); @@ -1532,12 +1557,40 @@ 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC util_lib/util.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util.deps -c -o util_lib/util.o util_lib/util.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +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/x86_64-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/x86_64-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, long unsigned int)' +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/x86_64-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/x86_64-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, long unsigned int)' +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 + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from util_lib/reformat_struc.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ + CC util_lib/util_aln_analyze.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c 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.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util.deps -c -o util_lib/util.o util_lib/util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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] @@ -1558,31 +1611,43 @@ 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/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 | } | ^ - CC util_lib/util_aln_analyze.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c +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.c: In function 'int dump_nfc(char*, char*)': +util_lib/util.c:4456:1: warning: no return statement in function returning non-void [-Wreturn-type] + 4456 | } + | ^ + CC util_lib/util_analyse_constraints_list.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_analyse_constraints_list.deps -c -o util_lib/util_analyse_constraints_list.o util_lib/util_analyse_constraints_list.c +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 | } + | ^ 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/x86_64-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/x86_64-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, long unsigned int)' -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/x86_64-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/x86_64-linux-gnu/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, long unsigned int)' +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 | } + | ^ + CC util_lib/util_constraints_list.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_constraints_list.deps -c -o util_lib/util_constraints_list.o util_lib/util_constraints_list.c 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 | } | ^ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c util_lib/reformat.c: In function 'Sequence* quick_read_seq(char*)': util_lib/reformat.c:1332:1: warning: control reaches end of non-void function [-Wreturn-type] 1332 | } @@ -1645,21 +1710,33 @@ util_lib/reformat.c:2507:1: warning: control reaches end of non-void function [-Wreturn-type] 2507 | } | ^ -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 - | ^~~~~~~ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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); | ~~~~~~~^~~~~~~~~~~~~~~~~ +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/reformat.c:3955:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3955 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ +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/reformat.c:3964:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3964 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ +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/reformat.c:3970:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3970 | fscanf ( fp, "%s",W->seq_name[a]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1669,6 +1746,10 @@ util_lib/reformat.c:3983:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3983 | fscanf ( fp, "\n"); | ~~~~~~~^~~~~~~~~~~ +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/reformat.c: In function 'Structure* read_rna_struc_number(Alignment*, char*)': util_lib/reformat.c:4256:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4256 | fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); @@ -1683,6 +1764,10 @@ util_lib/reformat.c:4507:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4507 | fscanf ( fp, "%s %d\n",S->name[S->nseq], &(S->len[S->nseq])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'FILE* get_number_list_in_file(FILE*, int*, int*, int*)': +util_lib/util.c:847:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 847 | fscanf ( fp, "%d",&list[n[0]++]); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4512:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4512 | fscanf ( fp, " %*c %c %*f %*f %*f\n",&(S->seq[S->nseq][a])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1694,15 +1779,32 @@ 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); | ~~~~~~~^~~~~~~~~~~~~~~ -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); - | ~~~~~~^~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from util_lib/util.c:52: + 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 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/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); + | ~~~~~~^~~~~~~~~~~~~ +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 'int fscanf_seq_name(FILE*, char*)': util_lib/reformat.c:5724:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 5724 | fscanf (fp, "%s", name); @@ -1726,125 +1828,18 @@ 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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ - CC util_lib/util_analyse_constraints_list.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_analyse_constraints_list.deps -c -o util_lib/util_analyse_constraints_list.o util_lib/util_analyse_constraints_list.c -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 | } - | ^ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -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 | } - | ^ - CC util_lib/util_constraints_list.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_constraints_list.deps -c -o util_lib/util_constraints_list.o util_lib/util_constraints_list.c -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); - | ~~~~~~~^~~~~~~~~~~~~~~~~ -util_lib/reformat.c:14307:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] -14307 | fscanf ( fp, "%d ", &value); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -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/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); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/reformat.c:14374:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] -14374 | fscanf ( fp, "%s ", buf); - | ~~~~~~~^~~~~~~~~~~~~~~~~ -util_lib/reformat.c:14387:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] -14387 | fscanf ( fp, "%d ", &value); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -util_lib/reformat.c:14414:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] -14414 | fscanf(fp, "\n"); - | ~~~~~~^~~~~~~~~~ -util_lib/reformat.c: In function 'int** read_pavie_matrix(char*)': -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); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 | } - | ^ -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]++]); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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 '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"); - | ~~~~~~~^~~~~~~~~~ - CC util_lib/util_declare.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/util.c: In function 'int perl_strstr(char*, char*)': util_lib/util.c:2468:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 2468 | fscanf (fp, "%d", &r); | ~~~~~~~^~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/util_constraints_list.c:37: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ util_lib/util.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_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.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]); @@ -1884,25 +1879,41 @@ util_lib/util.c:8528:10: warning: control reaches end of non-void function [-Wreturn-type] 8528 | myexit (EXIT_FAILURE); | ~~~~~~~^~~~~~~~~~~~~~ - CC util_lib/util_domain_constraints_list.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_domain_constraints_list.deps -c -o util_lib/util_domain_constraints_list.o util_lib/util_domain_constraints_list.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/util.c: In function 'int km_main(int, char**)': util_lib/util.c:10533:1: warning: control reaches end of non-void function [-Wreturn-type] 10533 | } | ^ -util_lib/util_constraints_list.c: In function 'Constraint_list* unfreeze_constraint_list(Constraint_list*)': -util_lib/util_constraints_list.c:1311:1: warning: no return statement in function returning non-void [-Wreturn-type] - 1311 | } +util_lib/reformat.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); + | ~~~~~~~^~~~~~~~~~~~~~~~~ +util_lib/reformat.c:14307:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] +14307 | fscanf ( fp, "%d ", &value); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ +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/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); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/reformat.c:14374:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] +14374 | fscanf ( fp, "%s ", buf); + | ~~~~~~~^~~~~~~~~~~~~~~~~ +util_lib/reformat.c:14387:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] +14387 | fscanf ( fp, "%d ", &value); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ +util_lib/reformat.c:14414:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] +14414 | fscanf(fp, "\n"); + | ~~~~~~^~~~~~~~~~ +util_lib/reformat.c: In function 'int** read_pavie_matrix(char*)': +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); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util_aln_analyze.c: In function 'Alignment* or_scan(Alignment*, Alignment*, char*)': +util_lib/util_aln_analyze.c:4480:1: warning: no return statement in function returning non-void [-Wreturn-type] + 4480 | } | ^ -util_lib/util_constraints_list.c: In function 'Constraint_list* fork_read_n_constraint_list(char**, int, char*, char*, char*, char*, FILE*, Constraint_list*, char*, int)': -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~~~~~~~~ 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); @@ -1923,25 +1934,32 @@ ./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 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 ./io_lib_header.h:33, + from util_lib/util_constraints_list.c:37: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ + CC util_lib/util_domain_constraints_list.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_domain_constraints_list.deps -c -o util_lib/util_domain_constraints_list.o util_lib/util_domain_constraints_list.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +util_lib/util_constraints_list.c: In function 'Constraint_list* unfreeze_constraint_list(Constraint_list*)': +util_lib/util_constraints_list.c:1311:1: warning: no return statement in function returning non-void [-Wreturn-type] + 1311 | } + | ^ +util_lib/util_constraints_list.c: In function 'Constraint_list* fork_read_n_constraint_list(char**, int, char*, char*, char*, char*, FILE*, Constraint_list*, char*, int)': +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~~~~~~ CC util_lib/util_dps.c -io_lib/tree_util.c: In function 'Sequence* get_nexus(char*)': -io_lib/tree_util.c:4597:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] - 4597 | sprintf (index, "%d", i); - | ^~ -io_lib/tree_util.c:4597:39: note: directive argument in the range [1, 2147483647] - 4597 | sprintf (index, "%d", i); - | ^~~~ -In file included from /usr/include/stdio.h:970, - from io_lib/tree_util.c:27: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Sequence* get_nexus(char*)' at io_lib/tree_util.c:4597:17: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 5 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_dps.deps -c -o util_lib/util_dps.o util_lib/util_dps.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ util_lib/util_constraints_list.c: In function 'Job_TC* submit_lib_job(Job_TC*)': @@ -1976,33 +1994,33 @@ 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); | ~~~~~~^~~~~~~~~~~~~~~~~ +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* 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: + 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_job_handling.deps -c -o util_lib/util_job_handling.o util_lib/util_job_handling.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -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_make_tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_make_tree.deps -c -o util_lib/util_make_tree.o util_lib/util_make_tree.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, - from util_lib/util_job_handling.c:33: + from util_lib/util_make_tree.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, - from util_lib/util_make_tree.c: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 | ^~~~~~~ @@ -2112,6 +2130,24 @@ 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); | ~~~~~~~~~^~~~~~ +io_lib/tree_util.c: In function 'Sequence* get_nexus(char*)': +io_lib/tree_util.c:4597:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] + 4597 | sprintf (index, "%d", i); + | ^~ +io_lib/tree_util.c:4597:39: note: directive argument in the range [1, 2147483647] + 4597 | sprintf (index, "%d", i); + | ^~~~ +In file included from /usr/include/stdio.h:970, + from io_lib/tree_util.c:27: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'Sequence* get_nexus(char*)' at io_lib/tree_util.c:4597:17: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 5 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function '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); @@ -2179,32 +2215,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c: In function 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)': -util_lib/util_constraints_list.c:694:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - 694 | sprintf ( aln_mode, "%s", method->aln_mode); - | ^~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)' at util_lib/util_constraints_list.c:694:11: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c: In function 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)': -util_lib/util_constraints_list.c:695:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - 695 | sprintf ( out_mode, "%s", method->out_mode); - | ^~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)' at util_lib/util_constraints_list.c:695:11: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ util_lib/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()); @@ -2234,28 +2244,26 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': -util_lib/aln_convertion_util.c:12147:32: warning: ' -w ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] -12147 | sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); - | ^~~~ -In file included from /usr/include/stdio.h:970, - from util_lib/aln_convertion_util.c:27: +util_lib/util_constraints_list.c: In function 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)': +util_lib/util_constraints_list.c:694:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + 694 | sprintf ( aln_mode, "%s", method->aln_mode); + | ^~ In function 'int sprintf(char*, const char*, ...)', - inlined from 'float** get_weight(Alignment*, Sequence*, char*)' at util_lib/aln_convertion_util.c:12147:15: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 1005) into a destination of size 1000 + inlined from 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)' at util_lib/util_constraints_list.c:694:11: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': -util_lib/aln_convertion_util.c:12141:32: warning: ' -i ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] -12141 | sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name); - | ^~~~ +util_lib/util_constraints_list.c: In function 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)': +util_lib/util_constraints_list.c:695:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + 695 | sprintf ( out_mode, "%s", method->out_mode); + | ^~ In function 'int sprintf(char*, const char*, ...)', - inlined from 'float** get_weight(Alignment*, Sequence*, char*)' at util_lib/aln_convertion_util.c:12141:15: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1009) into a destination of size 1000 + inlined from 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)' at util_lib/util_constraints_list.c:695:11: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, @@ -2304,6 +2312,34 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': +util_lib/aln_convertion_util.c:12147:32: warning: ' -w ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] +12147 | sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); + | ^~~~ +In file included from /usr/include/stdio.h:970, + from util_lib/aln_convertion_util.c:27: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'float** get_weight(Alignment*, Sequence*, char*)' at util_lib/aln_convertion_util.c:12147:15: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 1005) 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/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': +util_lib/aln_convertion_util.c:12141:32: warning: ' -i ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] +12141 | sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name); + | ^~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'float** get_weight(Alignment*, Sequence*, char*)' at util_lib/aln_convertion_util.c:12141:15: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1009) into a destination of size 1000 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function '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); @@ -2402,8 +2438,8 @@ dh_md5sums -O--sourcedirectory=t_coffee_source dh_builddeb -O--sourcedirectory=t_coffee_source dpkg-deb: building package 't-coffee-examples' in '../t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb'. -dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb'. dpkg-deb: building package 't-coffee' in '../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb'. +dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2411,12 +2447,14 @@ 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/2436871/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2436871/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/1959640 and its subdirectories -I: Current time: Fri Mar 27 03:19:53 -12 2026 -I: pbuilder-time-stamp: 1774624793 +I: removing directory /srv/workspace/pbuilder/2436871 and its subdirectories +I: Current time: Sat Feb 22 22:58:24 +14 2025 +I: pbuilder-time-stamp: 1740214704