Diff of the two buildlogs: -- --- b1/build.log 2024-05-02 08:35:19.091552622 +0000 +++ b2/build.log 2024-05-02 08:46:06.043968420 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed May 1 20:32:01 -12 2024 -I: pbuilder-time-stamp: 1714638721 +I: Current time: Thu May 2 22:35:46 +14 2024 +I: pbuilder-time-stamp: 1714638946 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying add_clean_target.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/26187/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/12340/tmp/hooks/D01_modify_environment starting +debug: Running on virt64c. +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 May 2 08:36 /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/12340/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/12340/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=3 ' - DISTRIBUTION='unstable' - 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]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(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=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='55093a54e8ca40f69924a1050b518a2d' - 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='26187' - PS1='# ' - PS2='> ' + INVOCATION_ID=690443912b024bb9862c10a3b1816fb6 + 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=12340 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.2bcvpqN9/pbuilderrc_Qm99 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2bcvpqN9/b1 --logfile b1/build.log paml_4.9j+dfsg-4.dsc' - SUDO_GID='113' - SUDO_UID='107' - 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.2bcvpqN9/pbuilderrc_kMiI --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2bcvpqN9/b2 --logfile b2/build.log paml_4.9j+dfsg-4.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 virt32a 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 2 07:43 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/26187/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 1 07:43 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/12340/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -141,7 +173,7 @@ Get: 28 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf debhelper all 13.15.3 [901 kB] -Fetched 18.4 MB in 0s (43.9 MB/s) +Fetched 18.4 MB in 3s (6468 kB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19440 files and directories currently installed.) @@ -276,7 +308,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/paml-4.9j+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 > ../paml_4.9j+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/12340/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/12340/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/paml-4.9j+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 > ../paml_4.9j+dfsg-4_source.changes dpkg-buildpackage: info: source package paml dpkg-buildpackage: info: source version 4.9j+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -288,7 +324,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/paml-4.9j+dfsg' dh_auto_clean - cd src && make -j3 clean + cd src && make -j4 clean make[2]: Entering directory '/build/reproducible-path/paml-4.9j+dfsg/src' rm -f baseml codeml basemlg mcmctree pamp evolver yn00 chi2 infinitesites make[2]: Leaving directory '/build/reproducible-path/paml-4.9j+dfsg/src' @@ -302,11 +338,12 @@ dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src dh_auto_build -O--sourcedirectory=src - cd src && make -j3 "INSTALL=install --strip-program=true" + cd src && make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/paml-4.9j+dfsg/src' cc -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/paml-4.9j+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -o baseml baseml.c tools.c -Wl,-z,relro -Wl,-z,now -lm cc -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/paml-4.9j+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -o codeml codeml.c tools.c -Wl,-z,relro -Wl,-z,now -lm cc -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/paml-4.9j+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -o basemlg basemlg.c tools.c -Wl,-z,relro -Wl,-z,now -lm +cc -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/paml-4.9j+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -o mcmctree mcmctree.c tools.c -Wl,-z,relro -Wl,-z,now -lm In file included from basemlg.c:80: treesub.c: In function 'ReadSeq': treesub.c:858:31: warning: passing argument 2 of 'printsma' from incompatible pointer type [-Wincompatible-pointer-types] @@ -326,6 +363,13 @@ paml.h:153:31: note: expected 'char **' but argument is of type 'unsigned char **' 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, | ~~~~~^~~~~~~~ +In file included from codeml.c:238: +treesub.c: In function 'IdenticalSeqs': +treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types] + 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); + | ~~~^~~~~~~ + | | + | char ** treesub.c: In function 'printPatterns': treesub.c:1093:25: warning: passing argument 2 of 'printsma' from incompatible pointer type [-Wincompatible-pointer-types] 1093 | printsma(fout, com.spname, com.z, com.ns, com.npatt, com.npatt, gap, com.seqtype, 1, 0, NULL); @@ -336,6 +380,10 @@ 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, | ~~~~~^~~~~~~~ treesub.c: In function 'AllPatterns': +In file included from codeml.c:17: +paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **' + 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); + | ~~~~~~~~~~~~~~~^~~~~~~~~ treesub.c:1361:25: warning: passing argument 2 of 'printsma' from incompatible pointer type [-Wincompatible-pointer-types] 1361 | printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 1, 0, NULL); | ~~~^~~~~~~ @@ -344,16 +392,16 @@ paml.h:153:31: note: expected 'char **' but argument is of type 'unsigned char **' 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, | ~~~~~^~~~~~~~ -In file included from baseml.c:131: +In file included from mcmctree.c:192: treesub.c: In function 'IdenticalSeqs': -In file included from codeml.c:238: +In file included from baseml.c:131: treesub.c: In function 'IdenticalSeqs': treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types] 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); | ~~~^~~~~~~ | | | char ** -In file included from baseml.c:11: +In file included from mcmctree.c:22: paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **' 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ @@ -362,7 +410,7 @@ | ~~~^~~~~~~ | | | char ** -In file included from codeml.c:17: +In file included from baseml.c:11: paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **' 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ @@ -394,6 +442,13 @@ treesub.c:3956:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3956 | fscanf(finitials, "%lf", &xin[i = 0]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c: In function 'ReadMorphology': +treesub.c:447:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 447 | fscanf(fin, "%s", com.spname[i]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c:450:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 450 | fscanf(fin, "%lf", &data.zmorph[locus][i][j]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadSeq': treesub.c:627:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fgets(line, lline, fseq); @@ -418,31 +473,27 @@ treesub.c:3151:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c: In function 'readx': -treesub.c:3956:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 3956 | fscanf(finitials, "%lf", &xin[i = 0]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c: In function 'Perturbation': -treesub.c:4565:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 4565 | fscanf(ftree, "%d%d", &i, &ntree); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c: In function 'StarDecomposition': -treesub.c:4867:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 4867 | fscanf(ftree, "%d%d", &i, &ntree); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c: In function 'rell': -treesub.c:5728:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 5728 | fscanf(flnf, "%d%d%d", &ntree0, &ls0, &npatt0); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c:5752:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 5752 | fscanf(flnf, "%d", &j); +treesub.c: In function 'ReadTreeSeqs': +treesub.c:8742:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 8742 | fscanf(ftree, "%d%d", &stree.nspecies, &i); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mcmctree.c: In function 'ReadBlengthGH': +mcmctree.c:840:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 840 | fscanf(fBGH, "%d", &i); | ^~~~~~~~~~~~~~~~~~~~~~ -treesub.c:5758:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 5758 | fscanf(flnf, "%d%d%lf", &j, &k, &y); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c:5763:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 5763 | fgets(line, lline, flnf); - | ^~~~~~~~~~~~~~~~~~~~~~~~ +mcmctree.c:861:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 861 | fscanf(fBGH, "%lf", &data.blMLE[locus][i]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mcmctree.c:868:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 868 | fscanf(fBGH, "%lf", &data.Gradient[locus][i]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mcmctree.c:870:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 870 | fscanf(fBGH, "%s", line); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +mcmctree.c: In function 'GenerateBlengthGH': +mcmctree.c:1028:7: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 1028 | system(line); + | ^~~~~~~~~~~~ treesub.c: In function 'ReadSeq': treesub.c:627:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fgets(line, lline, fseq); @@ -453,6 +504,13 @@ treesub.c:949:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mcmctree.c: In function 'Infinitesites': +mcmctree.c:1385:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 1385 | fscanf(fin, "%d", &i); + | ^~~~~~~~~~~~~~~~~~~~~ +mcmctree.c:1396:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 1396 | fscanf(fin, "%lf", &FixedDs[i]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'ReadTreeB': treesub.c:2812:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); @@ -467,36 +525,71 @@ treesub.c:3151:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c: In function 'ReadTreeSeqs': -treesub.c:8742:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 8742 | fscanf(ftree, "%d%d", &stree.nspecies, &i); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c: In function 'AdHocRateSmoothing': +treesub.c: In function 'ReadSeq': +treesub.c:627:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 627 | fgets(line, lline, fseq); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c:660:39: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); + | ^~~~~~~~~~~~~~~~~~~~~~~ +treesub.c:949:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 949 | fscanf(fseq, "%lf", &com.fpatt[h]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'readx': treesub.c:3956:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3956 | fscanf(finitials, "%lf", &xin[i = 0]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c:9574:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 9574 | fscanf(finStep1, "%lf", &x[i]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'Perturbation': treesub.c:4565:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 4565 | fscanf(ftree, "%d%d", &i, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c:9672:36: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 9672 | for (i = 0; i < com.np; i++) fscanf(finStep2, "%lf", &x[i]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'StarDecomposition': -treesub.c:9765:13: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 9765 | scanf("%lf", &Rj[j]); - | ^~~~~~~~~~~~~~~~~~~~ treesub.c:4867:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 4867 | fscanf(ftree, "%d%d", &i, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c: In function 'DatingHeteroData': -treesub.c:9884:10: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 9884 | scanf("%lf%d? ", &nu_AHRS, &nbrate); +treesub.c: In function 'ReadTreeB': +mcmctree.c: In function 'DescriptiveStatisticsSimpleMCMCTREE': +treesub.c:2812:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 2812 | fscanf(ftree, "%d", &tree.nbranch); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mcmctree.c:3824:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 3824 | fscanf(fin, "%lf", &dat[j*n + i]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c:2827:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2827 | if (popline) fgets(line, 254, ftree); + | ^~~~~~~~~~~~~~~~~~~~~~~ +treesub.c: In function 'ReadTreeN': +treesub.c:3091:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c:3151:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 3151 | fgets(line, lline, ftree); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c: In function 'rell': +treesub.c:5728:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 5728 | fscanf(flnf, "%d%d%d", &ntree0, &ls0, &npatt0); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c:5752:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 5752 | fscanf(flnf, "%d", &j); + | ^~~~~~~~~~~~~~~~~~~~~~ +treesub.c:5758:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 5758 | fscanf(flnf, "%d%d%lf", &j, &k, &y); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c: In function 'readx': +treesub.c:3956:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 3956 | fscanf(finitials, "%lf", &xin[i = 0]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c:5763:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 5763 | fgets(line, lline, flnf); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c: In function 'Perturbation': +treesub.c:4565:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 4565 | fscanf(ftree, "%d%d", &i, &ntree); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c: In function 'StarDecomposition': +treesub.c:4867:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 4867 | fscanf(ftree, "%d%d", &i, &ntree); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'rell': treesub.c:5728:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5728 | fscanf(flnf, "%d%d%d", &ntree0, &ls0, &npatt0); @@ -514,13 +607,31 @@ treesub.c:8742:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 8742 | fscanf(ftree, "%d%d", &stree.nspecies, &i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c: In function 'ReadTreeSeqs': +treesub.c:8742:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 8742 | fscanf(ftree, "%d%d", &stree.nspecies, &i); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c: In function 'AdHocRateSmoothing': +treesub.c:9574:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 9574 | fscanf(finStep1, "%lf", &x[i]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c:9672:36: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 9672 | for (i = 0; i < com.np; i++) fscanf(finStep2, "%lf", &x[i]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c:9765:13: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 9765 | scanf("%lf", &Rj[j]); + | ^~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'AdHocRateSmoothing': +treesub.c: In function 'DatingHeteroData': treesub.c:9574:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 9574 | fscanf(finStep1, "%lf", &x[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:9672:36: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 9672 | for (i = 0; i < com.np; i++) fscanf(finStep2, "%lf", &x[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c:9884:10: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 9884 | scanf("%lf%d? ", &nu_AHRS, &nbrate); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:9765:13: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 9765 | scanf("%lf", &Rj[j]); | ^~~~~~~~~~~~~~~~~~~~ @@ -568,96 +679,6 @@ tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cc -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/paml-4.9j+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -o mcmctree mcmctree.c tools.c -Wl,-z,relro -Wl,-z,now -lm -In file included from mcmctree.c:192: -treesub.c: In function 'IdenticalSeqs': -treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types] - 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); - | ~~~^~~~~~~ - | | - | char ** -In file included from mcmctree.c:22: -paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **' - 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); - | ~~~~~~~~~~~~~~~^~~~~~~~~ -treesub.c: In function 'ReadMorphology': -treesub.c:447:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 447 | fscanf(fin, "%s", com.spname[i]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c:450:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 450 | fscanf(fin, "%lf", &data.zmorph[locus][i][j]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c: In function 'ReadSeq': -treesub.c:627:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 627 | fgets(line, lline, fseq); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c:660:39: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); - | ^~~~~~~~~~~~~~~~~~~~~~~ -treesub.c:949:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 949 | fscanf(fseq, "%lf", &com.fpatt[h]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c: In function 'ReadTreeB': -treesub.c:2812:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 2812 | fscanf(ftree, "%d", &tree.nbranch); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c:2827:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2827 | if (popline) fgets(line, 254, ftree); - | ^~~~~~~~~~~~~~~~~~~~~~~ -treesub.c: In function 'ReadTreeN': -treesub.c:3091:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c:3151:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 3151 | fgets(line, lline, ftree); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c: In function 'ReadTreeSeqs': -treesub.c:8742:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 8742 | fscanf(ftree, "%d%d", &stree.nspecies, &i); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mcmctree.c: In function 'ReadBlengthGH': -mcmctree.c:840:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 840 | fscanf(fBGH, "%d", &i); - | ^~~~~~~~~~~~~~~~~~~~~~ -mcmctree.c:861:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 861 | fscanf(fBGH, "%lf", &data.blMLE[locus][i]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mcmctree.c:868:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 868 | fscanf(fBGH, "%lf", &data.Gradient[locus][i]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mcmctree.c:870:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 870 | fscanf(fBGH, "%s", line); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -mcmctree.c: In function 'GenerateBlengthGH': -mcmctree.c:1028:7: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 1028 | system(line); - | ^~~~~~~~~~~~ -mcmctree.c: In function 'Infinitesites': -mcmctree.c:1385:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 1385 | fscanf(fin, "%d", &i); - | ^~~~~~~~~~~~~~~~~~~~~ -mcmctree.c:1396:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 1396 | fscanf(fin, "%lf", &FixedDs[i]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mcmctree.c: In function 'DescriptiveStatisticsSimpleMCMCTREE': -mcmctree.c:3824:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 3824 | fscanf(fin, "%lf", &dat[j*n + i]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tools.c: In function 'gfopen': -tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 1148 | scanf("%s", filename); - | ^~~~~~~~~~~~~~~~~~~~~ -tools.c: In function 'scanfile': -tools.c:5356:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 5356 | fgets(line, lline, fin); - | ^~~~~~~~~~~~~~~~~~~~~~~ -tools.c: In function 'DescriptiveStatistics': -tools.c:5678:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 5678 | fscanf(fin, "%lf", &data[j*n + i]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:3861:54: warning: '%.6g' directive writing between 1 and 13 bytes into a region of size between 7 and 19 [-Wformat-overflow=] 3861 | sprintf(nodes[j].annotation, "[&95%%HPD={%.6g, %.6g}]", xHPD025[jj], xHPD975[jj]); | ^~~~ @@ -675,6 +696,21 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +tools.c: In function 'gfopen': +tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 1148 | scanf("%s", filename); + | ^~~~~~~~~~~~~~~~~~~~~ +tools.c: In function 'scanfile': +tools.c:5356:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 5356 | fgets(line, lline, fin); + | ^~~~~~~~~~~~~~~~~~~~~~~ +tools.c: In function 'DescriptiveStatistics': +tools.c:5678:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 5678 | fscanf(fin, "%lf", &data[j*n + i]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -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/paml-4.9j+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -o pamp pamp.c tools.c -Wl,-z,relro -Wl,-z,now -lm In file included from pamp.c:66: treesub.c: In function 'IdenticalSeqs': @@ -730,36 +766,6 @@ tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tools.c: In function 'gfopen': -tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 1148 | scanf("%s", filename); - | ^~~~~~~~~~~~~~~~~~~~~ -tools.c: In function 'scanfile': -tools.c:5356:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 5356 | fgets(line, lline, fin); - | ^~~~~~~~~~~~~~~~~~~~~~~ -tools.c: In function 'DescriptiveStatistics': -tools.c:5678:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 5678 | fscanf(fin, "%lf", &data[j*n + i]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tools.c: In function 'gfopen': -tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 1148 | scanf("%s", filename); - | ^~~~~~~~~~~~~~~~~~~~~ -tools.c: In function 'scanfile': -tools.c:5356:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 5356 | fgets(line, lline, fin); - | ^~~~~~~~~~~~~~~~~~~~~~~ -tools.c: In function 'DescriptiveStatistics': -tools.c:5678:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 5678 | fscanf(fin, "%lf", &data[j*n + i]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -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/paml-4.9j+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -o infinitesites -D INFINITESITES mcmctree.c tools.c -Wl,-z,relro -Wl,-z,now -lm In file included from mcmctree.c:192: treesub.c: In function 'IdenticalSeqs': @@ -835,6 +841,21 @@ mcmctree.c:3824:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 3824 | fscanf(fin, "%lf", &dat[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tools.c: In function 'gfopen': +tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 1148 | scanf("%s", filename); + | ^~~~~~~~~~~~~~~~~~~~~ +tools.c: In function 'scanfile': +tools.c:5356:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 5356 | fgets(line, lline, fin); + | ^~~~~~~~~~~~~~~~~~~~~~~ +tools.c: In function 'DescriptiveStatistics': +tools.c:5678:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 5678 | fscanf(fin, "%lf", &data[j*n + i]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -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/paml-4.9j+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -o evolver evolver.c tools.c -Wl,-z,relro -Wl,-z,now -lm In file included from evolver.c:66: treesub.c: In function 'ReadTreeB': @@ -1041,28 +1062,6 @@ evolver.c:1268:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1268 | fscanf(ftree, "%d%d", &i, &k); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cc -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/paml-4.9j+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -o yn00 yn00.c tools.c -Wl,-z,relro -Wl,-z,now -lm -In file included from yn00.c:70: -treesub.c: In function 'IdenticalSeqs': -treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types] - 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); - | ~~~^~~~~~~ - | | - | char ** -In file included from yn00.c:13: -paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **' - 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); - | ~~~~~~~~~~~~~~~^~~~~~~~~ -treesub.c: In function 'ReadSeq': -treesub.c:627:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 627 | fgets(line, lline, fseq); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -treesub.c:660:39: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); - | ^~~~~~~~~~~~~~~~~~~~~~~ -treesub.c:949:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 949 | fscanf(fseq, "%lf", &com.fpatt[h]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'gfopen': tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1148 | scanf("%s", filename); @@ -1095,6 +1094,28 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +cc -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/paml-4.9j+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -o yn00 yn00.c tools.c -Wl,-z,relro -Wl,-z,now -lm +In file included from yn00.c:70: +treesub.c: In function 'IdenticalSeqs': +treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types] + 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); + | ~~~^~~~~~~ + | | + | char ** +In file included from yn00.c:13: +paml.h:150:63: note: expected 'unsigned char **' but argument is of type 'char **' + 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); + | ~~~~~~~~~~~~~~~^~~~~~~~~ +treesub.c: In function 'ReadSeq': +treesub.c:627:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 627 | fgets(line, lline, fseq); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c:660:39: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); + | ^~~~~~~~~~~~~~~~~~~~~~~ +treesub.c:949:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 949 | fscanf(fseq, "%lf", &com.fpatt[h]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function 'gfopen': tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 1148 | scanf("%s", filename); @@ -1130,6 +1151,21 @@ chi2.c:54:10: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 54 | scanf ("%d%lf", &df, &chi2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +tools.c: In function 'gfopen': +tools.c:1148:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 1148 | scanf("%s", filename); + | ^~~~~~~~~~~~~~~~~~~~~ +tools.c: In function 'scanfile': +tools.c:5356:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 5356 | fgets(line, lline, fin); + | ^~~~~~~~~~~~~~~~~~~~~~~ +tools.c: In function 'DescriptiveStatistics': +tools.c:5678:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 5678 | fscanf(fin, "%lf", &data[j*n + i]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tools.c:5689:7: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/build/reproducible-path/paml-4.9j+dfsg/src' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp @@ -1186,9 +1222,9 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'paml' in '../paml_4.9j+dfsg-4_armhf.deb'. dpkg-deb: building package 'paml-dbgsym' in '../paml-dbgsym_4.9j+dfsg-4_armhf.deb'. dpkg-deb: building package 'paml-doc' in '../paml-doc_4.9j+dfsg-4_all.deb'. +dpkg-deb: building package 'paml' in '../paml_4.9j+dfsg-4_armhf.deb'. dpkg-genbuildinfo --build=binary -O../paml_4.9j+dfsg-4_armhf.buildinfo dpkg-genchanges --build=binary -O../paml_4.9j+dfsg-4_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1196,12 +1232,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/12340/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/12340/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/26187 and its subdirectories -I: Current time: Wed May 1 20:35:14 -12 2024 -I: pbuilder-time-stamp: 1714638914 +I: removing directory /srv/workspace/pbuilder/12340 and its subdirectories +I: Current time: Thu May 2 22:46:01 +14 2024 +I: pbuilder-time-stamp: 1714639561