Diff of the two buildlogs: -- --- b1/build.log 2023-04-26 12:09:01.387110267 +0000 +++ b2/build.log 2023-04-26 12:11:20.864922128 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 28 06:28:17 -12 2024 -I: pbuilder-time-stamp: 1716920897 +I: Current time: Thu Apr 27 02:09:04 +14 2023 +I: pbuilder-time-stamp: 1682510944 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./paml_4.9j+dfsg.orig.tar.xz] I: copying [./paml_4.9j+dfsg-4.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Dec 24 03:02:32 2022 -12 +gpgv: Signature made Sun Dec 25 05:02:32 2022 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key @@ -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/23953/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14446/tmp/hooks/D01_modify_environment starting +debug: Running on codethink16-arm64. +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 Apr 27 02:09 /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/14446/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14446/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='23953' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=14446 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.zxKT2MTQ/pbuilderrc_WiPA --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zxKT2MTQ/b1 --logfile b1/build.log paml_4.9j+dfsg-4.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.zxKT2MTQ/pbuilderrc_enAL --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zxKT2MTQ/b2 --logfile b2/build.log --extrapackages usrmerge paml_4.9j+dfsg-4.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink11-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 24 04:47 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/23953/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 27 00:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/14446/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 bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] -Fetched 18.3 MB in 0s (44.8 MB/s) +Fetched 18.3 MB in 0s (50.3 MB/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 ... 19616 files and directories currently installed.) @@ -275,8 +307,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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/14446/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/14446/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/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 @@ -327,6 +368,25 @@ 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); | ~~~~~~~~~~~~~~~^~~~~~~~~ +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] + 858 | printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 0, 0, NULL); + | ~~~^~~~~~~ + | | + | unsigned char ** +In file included from basemlg.c:11: +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, + | ~~~~~^~~~~~~~ +treesub.c:866:28: warning: passing argument 2 of 'printsma' from incompatible pointer type [-Wincompatible-pointer-types] + 866 | printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 0, 0, NULL); + | ~~~^~~~~~~ + | | + | unsigned char ** +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: treesub.c: In function 'IdenticalSeqs': treesub.c:1310:33: warning: passing argument 3 of 'printSeqs' from incompatible pointer type [-Wincompatible-pointer-types] @@ -338,76 +398,57 @@ 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); | ~~~~~~~~~~~~~~~^~~~~~~~~ -In file included from yn00.c:70: +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); + | ~~~^~~~~~~ + | | + | unsigned char ** +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 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 yn00.c:13: +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); | ~~~~~~~~~~~~~~~^~~~~~~~~ -In file included from codeml.c:238: +treesub.c: In function 'AllPatterns': +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); + | ~~~^~~~~~~ + | | + | unsigned char ** +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 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 codeml.c:17: +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); | ~~~~~~~~~~~~~~~^~~~~~~~~ -In file included from mcmctree.c:192: +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 ** -In file included from mcmctree.c:22: +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); | ~~~~~~~~~~~~~~~^~~~~~~~~ -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] - 858 | printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 0, 0, NULL); - | ~~~^~~~~~~ - | | - | unsigned char ** -In file included from basemlg.c:11: -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, - | ~~~~~^~~~~~~~ -treesub.c:866:28: warning: passing argument 2 of 'printsma' from incompatible pointer type [-Wincompatible-pointer-types] - 866 | printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 0, 0, NULL); - | ~~~^~~~~~~ - | | - | unsigned char ** -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, - | ~~~~~^~~~~~~~ -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); - | ~~~^~~~~~~ - | | - | unsigned char ** -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, - | ~~~~~^~~~~~~~ -treesub.c: In function 'AllPatterns': -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); - | ~~~^~~~~~~ - | | - | unsigned char ** -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, - | ~~~~~^~~~~~~~ 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); @@ -436,7 +477,6 @@ 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 'ReadTreeB': 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); @@ -444,23 +484,17 @@ 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 'GetNSfromTreeFile': +treesub.c:4159:16: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 4159 | fscanf(ftree, "%lf", &y); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +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 'GetNSfromTreeFile': -treesub.c:4159:16: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 4159 | fscanf(ftree, "%lf", &y); - | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function 'CladeSupport': treesub.c:4369:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 4369 | fscanf(fM, "%d%d", &i, &ntreeM); @@ -471,12 +505,24 @@ treesub.c:4419:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 4419 | fscanf(fM, "%d%d", &s, &ntreeM); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -evolver.c: In function 'main': treesub.c: In function 'ReadSeq': -pamp.c: In function 'main': -pamp.c:115:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 115 | fscanf(ftree, "%d%d", &i, &ntree); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 '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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +evolver.c: In function 'main': evolver.c:155:10: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 155 | scanf("%d", &option); | ^~~~~~~~~~~~~~~~~~~~ @@ -525,15 +571,6 @@ evolver.c:393:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 393 | fscanf(ftree, "%d%d", &com.ns, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c: In function 'TreeDistances': evolver.c:446:4: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 446 | scanf("%s", treef); @@ -544,10 +581,21 @@ evolver.c:458:4: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 458 | scanf("%d", &k); | ^~~~~~~~~~~~~~~ +pamp.c: In function 'main': +pamp.c:115:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 115 | fscanf(ftree, "%d%d", &i, &ntree); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c: In function 'GetDaa': evolver.c:638:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 638 | fscanf(fdaa, "%lf", &daa[i*n + j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c: In function 'Simulate': evolver.c:809:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 809 | fscanf(fin, "%d", &format); @@ -657,17 +705,6 @@ evolver.c:970:40: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 970 | fscanf(fin, "%d", &com.icode); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ -evolver.c: In function 'CladeMrBayesProbabilities': -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); @@ -675,6 +712,10 @@ treesub.c:3151:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ +evolver.c: In function 'CladeMrBayesProbabilities': +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]); @@ -731,13 +772,6 @@ 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]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -748,6 +782,13 @@ 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); @@ -792,9 +833,6 @@ 5763 | fgets(line, lline, flnf); | ^~~~~~~~~~~~~~~~~~~~~~~~ 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 'ReadSeq': treesub.c:627:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 627 | fgets(line, lline, fseq); @@ -805,6 +843,9 @@ 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: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]); @@ -815,17 +856,17 @@ 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 'DatingHeteroData': treesub.c: In function 'ReadTreeB': -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:2812:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +treesub.c: In function 'DatingHeteroData': 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: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 '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); @@ -1186,8 +1227,8 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'paml-dbgsym' in '../paml-dbgsym_4.9j+dfsg-4_arm64.deb'. dpkg-deb: building package 'paml' in '../paml_4.9j+dfsg-4_arm64.deb'. +dpkg-deb: building package 'paml-dbgsym' in '../paml-dbgsym_4.9j+dfsg-4_arm64.deb'. dpkg-deb: building package 'paml-doc' in '../paml-doc_4.9j+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary -O../paml_4.9j+dfsg-4_arm64.buildinfo dpkg-genchanges --build=binary -O../paml_4.9j+dfsg-4_arm64.changes @@ -1196,12 +1237,14 @@ 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/14446/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14446/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/23953 and its subdirectories -I: Current time: Tue May 28 06:32:00 -12 2024 -I: pbuilder-time-stamp: 1716921120 +I: removing directory /srv/workspace/pbuilder/14446 and its subdirectories +I: Current time: Thu Apr 27 02:11:19 +14 2023 +I: pbuilder-time-stamp: 1682511079