Diff of the two buildlogs: -- --- b1/build.log 2025-01-05 16:00:20.220212370 +0000 +++ b2/build.log 2025-01-05 16:07:07.905589736 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jan 5 03:53:09 -12 2025 -I: pbuilder-time-stamp: 1736092389 +I: Current time: Mon Jan 6 06:00:52 +14 2025 +I: pbuilder-time-stamp: 1736092852 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -37,52 +37,84 @@ 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/17259/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/18506/tmp/hooks/D01_modify_environment starting +debug: Running on virt32a. +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 Jan 5 16:01 /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/18506/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/18506/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='faeefd3dece64baa9f115eb443ef5cad' - 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='17259' - PS1='# ' - PS2='> ' + INVOCATION_ID=87516425d6654970b52d9de169073775 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=18506 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.LCtg4oM2/pbuilderrc_J0SD --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.LCtg4oM2/b1 --logfile b1/build.log t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc' - SUDO_GID='114' - SUDO_UID='109' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.LCtg4oM2/pbuilderrc_QLFC --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.LCtg4oM2/b2 --logfile b2/build.log t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux ff64a 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/17259/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/18506/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -147,7 +179,7 @@ Get: 27 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf debhelper all 13.23 [919 kB] -Fetched 19.1 MB in 1s (29.2 MB/s) +Fetched 19.1 MB in 1s (31.4 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 ... 19679 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/18506/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/18506/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 @@ -305,48 +341,60 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_auto_build -- USER_BIN=../bin/ FCC="gfortran -g -O2 -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection" 'CC=$(CXX)' all - cd t_coffee_source && make -j5 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection" CC=\$\(CXX\) all + cd t_coffee_source && make -j4 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -ffile-prefix-map=/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -fstack-clash-protection" CC=\$\(CXX\) all make[2]: Entering directory '/build/reproducible-path/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/t_coffee_source' CC dev_lib/dev1.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dev_lib/dev1.deps -c -o dev_lib/dev1.o dev_lib/dev1.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/evaluate.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c CC dp_lib/evaluate_dirichlet.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c - CC dp_lib/evaluate_for_domain.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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/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/evaluate_for_domain.c:33: + from dp_lib/evaluate_dirichlet.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/evaluate_dirichlet.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 | ^~~~~~~ +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 dev_lib/dev1.c:33: + from dp_lib/evaluate.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ +dp_lib/evaluate_dirichlet.c: In function 'Mixture* read_dirichlet(char*)': +dp_lib/evaluate_dirichlet.c:317:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 317 | fscanf(fp, "%f\n", &f); + | ~~~~~~^~~~~~~~~~~~~~~~ +dp_lib/evaluate_dirichlet.c:319:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 319 | fscanf(fp, "%f", &f); + | ~~~~~~^~~~~~~~~~~~~~ +dp_lib/evaluate_dirichlet.c:323:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 323 | fscanf(fp, "%f", &f); + | ~~~~~~^~~~~~~~~~~~~~ +dp_lib/evaluate_dirichlet.c:326:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 326 | fscanf(fp, "\n"); + | ~~~~~~^~~~~~~~~~ + CC dp_lib/evaluate_for_domain.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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); @@ -372,23 +420,6 @@ | | | | int double | %3f -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_dirichlet.c: In function 'Mixture* read_dirichlet(char*)': -dp_lib/evaluate_dirichlet.c:317:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 317 | fscanf(fp, "%f\n", &f); - | ~~~~~~^~~~~~~~~~~~~~~~ -dp_lib/evaluate_dirichlet.c:319:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 319 | fscanf(fp, "%f", &f); - | ~~~~~~^~~~~~~~~~~~~~ -dp_lib/evaluate_dirichlet.c:323:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 323 | fscanf(fp, "%f", &f); - | ~~~~~~^~~~~~~~~~~~~~ -dp_lib/evaluate_dirichlet.c:326:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 326 | fscanf(fp, "\n"); - | ~~~~~~^~~~~~~~~~ CC dp_lib/evaluate_for_struc.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ @@ -402,13 +433,23 @@ 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/fsa_dp.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o dp_lib/fsa_dp.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +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 + | ^~~~~~~ dp_lib/evaluate.c: In function 'float** initialise_aa_physico_chemical_property_table(int*)': dp_lib/evaluate.c:7626:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 7626 | fscanf (fp, "%f %c %*s",&v1, &c1 ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/evaluate_for_struc.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ + CC dp_lib/fsa_dp.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o dp_lib/fsa_dp.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC dp_lib/pavie_dp.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ @@ -422,11 +463,6 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/evaluate_for_struc.c:34: -./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++]); @@ -442,9 +478,6 @@ 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/showpair.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ 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); @@ -473,6 +506,9 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ + CC dp_lib/showpair.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ 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 @@ -481,11 +517,6 @@ CC dp_lib/util_domain_dp.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o dp_lib/util_domain_dp.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -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 - | ^~~~~~~ CC dp_lib/util_domain_dp_drivers.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ @@ -497,6 +528,16 @@ CC dp_lib/util_dp_cdna_fasta_nw.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ +In file included from ./io_lib_header.h:33, + from dp_lib/util_domain_dp.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_cdna_fasta_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_clean_maln.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ @@ -504,7 +545,7 @@ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_cdna_fasta_nw.c:33: + from dp_lib/util_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ @@ -513,14 +554,6 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_drivers.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ - CC dp_lib/util_dp_est.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ 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; @@ -604,19 +637,19 @@ 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)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ + CC dp_lib/util_dp_est.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_est.c: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 | ^~~~~~~ - CC dp_lib/util_dp_fasta_sw.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_fasta_nw.c:34: + from dp_lib/util_dp_est.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ @@ -665,8 +698,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - CC dp_lib/util_dp_generic_fasta_nw.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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_fasta_sw.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ dp_lib/util_dp_drivers.c: In function '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=] @@ -686,14 +719,9 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC dp_lib/util_dp_gotoh_nw.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_nw.deps -c -o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_nw.c + CC dp_lib/util_dp_generic_fasta_nw.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_generic_fasta_nw.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ dp_lib/util_dp_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); @@ -708,16 +736,21 @@ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_gotoh_nw.c:34: + from dp_lib/util_dp_generic_fasta_nw.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ + CC dp_lib/util_dp_gotoh_nw.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ CC dp_lib/util_dp_gotoh_sw.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_gotoh_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_gotoh_sw.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -727,17 +760,14 @@ 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_mm_nw.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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_mm_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_sim.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ 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); @@ -751,11 +781,22 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ + CC dp_lib/util_dp_sim.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_sim.c:32: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_ssec_pwaln.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ dp_lib/util_dp_sim.c: In function 'int addnode(int, int, int, int, int, int, int)': dp_lib/util_dp_sim.c:173:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 173 | register int d; @@ -936,11 +977,6 @@ 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 - | ^~~~~~~ CC dp_lib/util_dp_suboptimal_nw.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ @@ -952,16 +988,16 @@ CC dp_lib/util_graph_maln.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ - CC fastal/diagonal.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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: + from dp_lib/util_graph_maln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ + CC fastal/diagonal.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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_graph_maln.c:33: + from fastal/diagonal.c:31: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ @@ -979,21 +1015,61 @@ 441 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ CC fastal/fastal.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC fastal/fastal_opt_parsing.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ CC fastal/iteration.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC fastal/parttree.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ 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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.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 + | ^~~~~~~ +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c: In function 'void iterate(Fastal_param*, void*, char*, char*, int)': +fastal/iteration.c:310:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 310 | fgets(line, LINE_LENGTH , alignment_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:435:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 435 | system(command); + | ~~~~~~^~~~~~~~~ +fastal/iteration.c: In function 'void write_iterated_aln(char*, char*, char*, char*, int*, int, char*, int*, int)': +fastal/iteration.c:501:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 501 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:504:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 504 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:535:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 535 | fgets(alnline, ALNLINE_LENGTH, old_aln_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c: In function 'void edit2seq_pattern(FILE*, char*, char*)': +fastal/iteration.c:563:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:565:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 565 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:567:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 567 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:569:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 569 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function 'int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:1924:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1924 | system(blast_command); @@ -1027,7 +1103,6 @@ fastal/fastal.c:2262:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2262 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fastal/fastal.c: In function 'void file_pos2profile(FILE*, long int, Fastal_profile*, int, Fastal_param*)': fastal/fastal.c:3201:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3201 | fgets (line, LINE_LENGTH , seq_file); @@ -1071,48 +1146,6 @@ fastal/fastal.c:3643:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3643 | fgets(aligned_sequence, alignment_length+3, edit_seq_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC fastal/scoring.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/scoring.deps -c -o fastal/scoring.o fastal/scoring.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -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 - | ^~~~~~~ -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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c: In function 'void iterate(Fastal_param*, void*, char*, char*, int)': -fastal/iteration.c:310:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 310 | fgets(line, LINE_LENGTH , alignment_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:435:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 435 | system(command); - | ~~~~~~^~~~~~~~~ -fastal/iteration.c: In function 'void write_iterated_aln(char*, char*, char*, char*, int*, int, char*, int*, int)': -fastal/iteration.c:501:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 501 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:504:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 504 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:535:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 535 | fgets(alnline, ALNLINE_LENGTH, old_aln_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c: In function 'void edit2seq_pattern(FILE*, char*, char*)': -fastal/iteration.c:563:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:565:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 565 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:567:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 567 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:569:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 569 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from fastal/parttree.c:36: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -1156,14 +1189,14 @@ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC fastal/scoring.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/scoring.deps -c -o fastal/scoring.o fastal/scoring.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, from fastal/scoring.c:37: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC fastal/tree.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ fastal/scoring.c: In function 'double calculate_sum_of_pairs_score_affine(char*, int**, double, double)': fastal/scoring.c:76:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | fgets(line, LINE_LENGTH, alignment_file); @@ -1198,14 +1231,6 @@ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 - | ^~~~~~~ - CC io_lib/io_func.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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/scoring.c: In function 'int complete_agreement_score(char*, const char*)': fastal/scoring.c:624:49: warning: '%s' directive writing up to 499 bytes into a region of size 200 [-Wformat-overflow=] 624 | sprintf(ref_file_name, "%s/%s",directory, dp->d_name); @@ -1221,23 +1246,26 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ + CC fastal/tree.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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 io_lib/io_func.c:33: + from fastal/tree.c:33: ./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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c + CC io_lib/io_func.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ -io_lib/io_func.c: In function 'int output_raw_score(Alignment*, Alignment*, char*)': -io_lib/io_func.c:1235:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null] - 1235 | if (!A)return NULL; - | ^~~~ In file included from ./io_lib_header.h:33, - from io_lib/pb_util_read_seq_util.c:34: + from io_lib/io_func.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ +io_lib/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 | } @@ -1250,6 +1278,14 @@ 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_seq_util.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ +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 + | ^~~~~~~ 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; @@ -1334,9 +1370,6 @@ CC io_lib/tree_util.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, from io_lib/tree_util.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -1378,9 +1411,6 @@ io_lib/tree_util.c:7204:1: warning: no return statement in function returning non-void [-Wreturn-type] 7204 | } | ^ - CC km_coffee/Vector.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ io_lib/tree_util.c: In function 'char* graph2cons_d(long unsigned int, int)': io_lib/tree_util.c:10163:27: warning: NULL used in arithmetic [-Wpointer-arith] 10163 | while ((c=rn_c(s))!=NULL) @@ -1398,12 +1428,8 @@ io_lib/tree_util.c:9947:46: note: declared here 9947 | void wn_c (unsigned long n, unsigned long t); | ~~~~~~~~~~~~~~^ - CC km_coffee/classes.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC km_coffee/km_coffee.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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/Stack.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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/tree_util.c: In function 'FILE* create_tree(NT_node, NT_node, int*, int*, int*, tnode***, FILE*)': io_lib/tree_util.c:3973:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3973 | fscanf(fp,"%f",&dist); @@ -1411,12 +1437,19 @@ io_lib/tree_util.c:3981:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3981 | fscanf(fp,"%f",&bootstrap); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ io_lib/tree_util.c: In function 'int check_node(ALN_node, char*)': io_lib/tree_util.c:9772:1: warning: control reaches end of non-void function [-Wreturn-type] 9772 | } | ^ - CC km_coffee/km_util.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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/Vector.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ + CC km_coffee/classes.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ + CC km_coffee/km_coffee.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ In file included from ./io_lib_header.h:33, from km_coffee/km_coffee.c:43: @@ -1494,6 +1527,15 @@ 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/km_util.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ + CC km_coffee/kmeans.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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 +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ km_coffee/km_util.c: In function 'void* my_malloc(size_t)': km_coffee/km_util.c:49:76: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 49 | fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size); @@ -1523,28 +1565,14 @@ | ~^ | | | char* - CC km_coffee/kmeans.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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 -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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 CC util_lib/aln_compare.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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 - | ^~~~~~~ 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 | ^~~~~~~ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 | } @@ -1562,22 +1590,10 @@ 6816 | } | ^ In file included from ./io_lib_header.h:33, - from util_lib/aln_convertion_util.c:33: + from util_lib/aln_compare.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -util_lib/aln_convertion_util.c: In function 'int trim_aln_file(char*, char*, char*, char*)': -util_lib/aln_convertion_util.c:3105:62: warning: NULL used in arithmetic [-Wpointer-arith] - 3105 | while ((get_next_fasta_sequence(fp, &name, &comment,&seq)!=NULL)) - | ^~~~ -util_lib/aln_convertion_util.c: In function 'Alignment* aln2conservation(Alignment*, int, char*)': -util_lib/aln_convertion_util.c:4511:1: warning: no return statement in function returning non-void [-Wreturn-type] - 4511 | } - | ^ -util_lib/aln_convertion_util.c: In function 'Alignment* aln2N_replicate(Alignment*, char*, char*)': -util_lib/aln_convertion_util.c:7762:1: warning: no return statement in function returning non-void [-Wreturn-type] - 7762 | } - | ^ In file included from /usr/include/string.h:548, from t_coffee_lib/t_coffee.c:32: In function 'char* strcpy(char*, const char*)', @@ -1592,6 +1608,44 @@ 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:81:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, unsigned int)' + CC util_lib/aln_convertion_util.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ +t_coffee_lib/t_coffee.c: In function 'int batch_main(int, char**)': +t_coffee_lib/t_coffee.c:5662:66: warning: '%s' directive writing up to 999 bytes into a region of size between 982 and 991 [-Wformat-overflow=] + 5662 | sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); + | ^~ ~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:970, + from t_coffee_lib/t_coffee.c:27: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int batch_main(int, char**)' at t_coffee_lib/t_coffee.c:5662:18: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1018) into a destination of size 1000 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +In file included from ./io_lib_header.h:33, + from util_lib/aln_convertion_util.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +util_lib/aln_convertion_util.c: In function 'int trim_aln_file(char*, char*, char*, char*)': +util_lib/aln_convertion_util.c:3105:62: warning: NULL used in arithmetic [-Wpointer-arith] + 3105 | while ((get_next_fasta_sequence(fp, &name, &comment,&seq)!=NULL)) + | ^~~~ +util_lib/aln_convertion_util.c: In function 'Alignment* aln2conservation(Alignment*, int, char*)': +util_lib/aln_convertion_util.c:4511:1: warning: no return statement in function returning non-void [-Wreturn-type] + 4511 | } + | ^ +util_lib/aln_convertion_util.c: In function 'Alignment* aln2N_replicate(Alignment*, char*, char*)': +util_lib/aln_convertion_util.c:7762:1: warning: no return statement in function returning non-void [-Wreturn-type] + 7762 | } + | ^ + CC util_lib/hsearch.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ 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); @@ -1602,18 +1656,18 @@ 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC util_lib/hsearch.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ -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); - | ^~ ~~~~~~~~~~~~ +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 t_coffee_lib/t_coffee.c:27: + from io_lib/tree_util.c:27: In function 'int sprintf(char*, const char*, ...)', - inlined from 'int batch_main(int, char**)' at t_coffee_lib/t_coffee.c:5662:18: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1018) into a destination of size 1000 + inlined from 'Sequence* get_nexus(char*)' at io_lib/tree_util.c:4597:17: +/usr/include/arm-linux-gnueabihf/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, @@ -1636,9 +1690,6 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC util_lib/reformat_struc.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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/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 | } @@ -1647,11 +1698,6 @@ util_lib/reformat.c:14453:1: warning: no return statement in function returning non-void [-Wreturn-type] 14453 | } | ^ -In file included from ./io_lib_header.h:33, - from util_lib/reformat_struc.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ 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 | } @@ -1702,10 +1748,6 @@ util_lib/reformat.c:1493:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1493 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ -util_lib/reformat_struc.c: In function 'void bfactor2x_in_pdb(char*, char*, float*)': -util_lib/reformat_struc.c:125:25: warning: too many arguments for format [-Wformat-extra-args] - 125 | fprintf (out, "ATOM ", lw[1]);//ATOM - | ^~~~~~~~ util_lib/reformat.c: In function 'int is_pdb_name(char*)': util_lib/reformat.c:1788:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1788 | fscanf ( fp, "%d", &result); @@ -1789,25 +1831,6 @@ util_lib/reformat.c:6511:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 6511 | fscanf (fp, "%s %d", name,&i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -util_lib/reformat_struc.c: In function 'Ca_trace* simple_read_ca_trace(char*)': -util_lib/reformat_struc.c:370:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 370 | fscanf ( fp, "%*s" ); - | ~~~~~~~^~~~~~~~~~~~~ -util_lib/reformat_struc.c:372:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 372 | fscanf ( fp, "%*s" ); - | ~~~~~~~^~~~~~~~~~~~~ -util_lib/reformat_struc.c:378:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 378 | fscanf (fp, "%*s %*s %c %*c %d %*f %*f %*f\n",&res,&res_num); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/reformat_struc.c:405:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 405 | fscanf ( fp, "%*s" ); - | ~~~~~~~^~~~~~~~~~~~~ -util_lib/reformat_struc.c:407:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 407 | fscanf ( fp, "%*s" ); - | ~~~~~~~^~~~~~~~~~~~~ -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); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -1835,30 +1858,40 @@ 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/arm-linux-gnueabihf/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 ()); - | ~~~~~~~~~~~~~~~~~ + CC util_lib/reformat_struc.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +In file included from ./io_lib_header.h:33, + from util_lib/reformat_struc.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +util_lib/reformat_struc.c: In function 'void bfactor2x_in_pdb(char*, char*, float*)': +util_lib/reformat_struc.c:125:25: warning: too many arguments for format [-Wformat-extra-args] + 125 | fprintf (out, "ATOM ", lw[1]);//ATOM + | ^~~~~~~~ +util_lib/reformat_struc.c: In function 'Ca_trace* simple_read_ca_trace(char*)': +util_lib/reformat_struc.c:370:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 370 | fscanf ( fp, "%*s" ); + | ~~~~~~~^~~~~~~~~~~~~ +util_lib/reformat_struc.c:372:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 372 | fscanf ( fp, "%*s" ); + | ~~~~~~~^~~~~~~~~~~~~ +util_lib/reformat_struc.c:378:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 378 | fscanf (fp, "%*s %*s %c %*c %d %*f %*f %*f\n",&res,&res_num); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/reformat_struc.c:405:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 405 | fscanf ( fp, "%*s" ); + | ~~~~~~~^~~~~~~~~~~~~ +util_lib/reformat_struc.c:407:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 407 | fscanf ( fp, "%*s" ); + | ~~~~~~~^~~~~~~~~~~~~ +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); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util.deps -c -o util_lib/util.o util_lib/util.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ - CC util_lib/util_aln_analyze.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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 @@ -1968,15 +2001,18 @@ util_lib/util.c:8528:10: warning: control reaches end of non-void function [-Wreturn-type] 8528 | myexit (EXIT_FAILURE); | ~~~~~~~^~~~~~~~~~~~~~ +util_lib/util.c: In function 'int km_main(int, char**)': +util_lib/util.c:10533:1: warning: control reaches end of non-void function [-Wreturn-type] +10533 | } + | ^ + CC util_lib/util_aln_analyze.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, from util_lib/util_aln_analyze.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -util_lib/util.c: In function 'int km_main(int, char**)': -util_lib/util.c:10533:1: warning: control reaches end of non-void function [-Wreturn-type] -10533 | } - | ^ 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 | } @@ -2013,8 +2049,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - CC util_lib/util_analyse_constraints_list.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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 In file included from /usr/include/stdio.h:970, from util_lib/util_aln_analyze.c:27: In function 'int sprintf(char*, const char*, ...)', @@ -2041,7 +2075,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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()); @@ -2071,39 +2104,28 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/util_analyse_constraints_list.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ - CC util_lib/util_constraints_list.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_constraints_list.deps -c -o util_lib/util_constraints_list.o util_lib/util_constraints_list.c - CC util_lib/util_declare.c -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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/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); + | ^~~~~~~~~ +In file included from /usr/include/stdio.h:970, + from util_lib/reformat.c:27: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)' at util_lib/reformat.c:13639:13: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 64 or more bytes (assuming 3059) 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:11638:32: warning: '%s' directive argument is null [-Wformat-overflow=] +11638 | sprintf (type, "%s", ACTION (2)); + | ^~ + CC util_lib/util_analyse_constraints_list.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_analyse_constraints_list.deps -c -o util_lib/util_analyse_constraints_list.o util_lib/util_analyse_constraints_list.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -In file included from ./io_lib_header.h:33, - from util_lib/util_declare.c:37: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/util_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_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); - | ^~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* get_mcoffee_4_tcoffee()': util_lib/util.c:5400:44: warning: '/mcoffee/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); @@ -2146,6 +2168,39 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ + CC util_lib/util_constraints_list.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ +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 + | ^~~~~~~ + CC util_lib/util_declare.c +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +In file included from ./io_lib_header.h:33, + from util_lib/util_constraints_list.c:37: +./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_declare.c:37: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +util_lib/util_constraints_list.c: In function 'Constraint_list* unfreeze_constraint_list(Constraint_list*)': +util_lib/util_constraints_list.c:1311:1: warning: no return statement in function returning non-void [-Wreturn-type] + 1311 | } + | ^ +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); + | ^~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'Job_TC* submit_lib_job(Job_TC*)': util_lib/util_constraints_list.c:582:19: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 582 | chdir (tdir); @@ -2201,51 +2256,6 @@ util_lib/util.c:8658:68: warning: '%s' directive argument is null [-Wformat-overflow=] 8658 | fprintf ( io, "\n\t#### File Type= %-15s Format= %-15s Name= %s",type, format, name ); | ^~ -util_lib/reformat.c: In function 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)': -util_lib/reformat.c:13639:34: warning: ' -method ' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] -13639 | sprintf ( command, "%s -method %s -aln %s -tree %s -dmatrix %s -weightfile %s %s",method_4_msa_weights, action_list[1],aln_name, tree_name, dist_matrix_name,weight_name, TO_NULL_DEVICE); - | ^~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from util_lib/reformat.c:27: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)' at util_lib/reformat.c:13639:13: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 64 or more bytes (assuming 3059) 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:11638:32: warning: '%s' directive argument is null [-Wformat-overflow=] -11638 | sprintf (type, "%s", ACTION (2)); - | ^~ -util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': -util_lib/util_constraints_list.c:4922:26: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - 4922 | sprintf ( mode, "%s", (CL && in_mode==NULL)?CL->distance_matrix_mode:in_mode); - | ^~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4922:10: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': -util_lib/util_constraints_list.c:4923:30: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - 4923 | sprintf ( sim_mode, "%s", (CL && in_sim_mode==NULL)?CL->distance_matrix_sim_mode:in_sim_mode); - | ^~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4923:10: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ CC util_lib/util_domain_constraints_list.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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++ @@ -2260,6 +2270,11 @@ CC util_lib/util_job_handling.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -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 + | ^~~~~~~ util_lib/util.c: In function 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)': util_lib/util.c:5400:44: warning: '/mcoffee/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); @@ -2291,19 +2306,40 @@ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from util_lib/util_dps.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 | ^~~~~~~ +util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': +util_lib/util_constraints_list.c:4922:26: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + 4922 | sprintf ( mode, "%s", (CL && in_mode==NULL)?CL->distance_matrix_mode:in_mode); + | ^~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4922:10: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': +util_lib/util_constraints_list.c:4923:30: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + 4923 | sprintf ( sim_mode, "%s", (CL && in_sim_mode==NULL)?CL->distance_matrix_sim_mode:in_sim_mode); + | ^~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4923:10: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ CC util_lib/util_make_tree.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_make_tree.deps -c -o util_lib/util_make_tree.o util_lib/util_make_tree.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ./io_lib_header.h:33, - from util_lib/util_job_handling.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, from util_lib/util_make_tree.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol @@ -2488,9 +2524,9 @@ dh_gencontrol -O--sourcedirectory=t_coffee_source dh_md5sums -O--sourcedirectory=t_coffee_source dh_builddeb -O--sourcedirectory=t_coffee_source -dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_armhf.deb'. dpkg-deb: building package 't-coffee' in '../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_armhf.deb'. dpkg-deb: building package 't-coffee-examples' in '../t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb'. +dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_armhf.buildinfo dpkg-genchanges --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2498,12 +2534,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/18506/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/18506/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/17259 and its subdirectories -I: Current time: Sun Jan 5 04:00:15 -12 2025 -I: pbuilder-time-stamp: 1736092815 +I: removing directory /srv/workspace/pbuilder/18506 and its subdirectories +I: Current time: Mon Jan 6 06:07:02 +14 2025 +I: pbuilder-time-stamp: 1736093222