Diff of the two buildlogs: -- --- b1/build.log 2023-04-13 21:53:48.377878101 +0000 +++ b2/build.log 2023-04-13 21:54:49.211177992 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Apr 13 09:52:31 -12 2023 -I: pbuilder-time-stamp: 1681422751 +I: Current time: Thu May 16 18:16:51 +14 2024 +I: pbuilder-time-stamp: 1715833011 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 [./lagan_2.0.orig.tar.gz] I: copying [./lagan_2.0-9.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Aug 6 20:35:08 2022 -12 +gpgv: Signature made Sun Aug 7 22:35:08 2022 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key @@ -37,11 +37,20 @@ dpkg-source: info: applying gcc-lto.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/30179/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/30597/tmp/hooks/D01_modify_environment starting +debug: Running on codethink13-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 +lrwxrwxrwx 1 root root 4 Jan 6 2023 /bin/sh -> dash +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/30597/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/30597/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' + 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' @@ -51,38 +60,38 @@ IFS=' ' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='30179' + PPID='30597' PS1='# ' PS2='> ' 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.kqJCGcRr/pbuilderrc_BmGo --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.kqJCGcRr/b1 --logfile b1/build.log lagan_2.0-9.dsc' + 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.kqJCGcRr/pbuilderrc_xFHC --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.kqJCGcRr/b2 --logfile b2/build.log --extrapackages usrmerge lagan_2.0-9.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a - Linux codethink16-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 10 22:26 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/30179/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 14 06:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/30597/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -152,7 +161,7 @@ Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libboost1.74-dev arm64 1.74.0+ds1-20 [9510 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libboost-dev arm64 1.74.0.3 [4548 B] -Fetched 27.9 MB in 1s (49.6 MB/s) +Fetched 27.9 MB in 1s (49.3 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.) @@ -294,8 +303,17 @@ 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/lagan-2.0/ && 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 > ../lagan_2.0-9_source.changes +I: user script /srv/workspace/pbuilder/30597/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/30597/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/lagan-2.0/ && 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 > ../lagan_2.0-9_source.changes dpkg-buildpackage: info: source package lagan dpkg-buildpackage: info: source version 2.0-9 dpkg-buildpackage: info: source distribution unstable @@ -340,6 +358,10 @@ gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2mf utils/bin2mf.c -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2bl utils/bin2bl.c -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cextract utils/cextract.c -Wl,-z,relro +anchors.c: In function 'anchors_getline': +anchors.c:232:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 232 | fgets(temp, 1024, infile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ order.c: In function 'doAlign': order.c:409:5: warning: implicit declaration of function 'printMFAAlign'; did you mean 'printBinAlign'? [-Wimplicit-function-declaration] 409 | printMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); @@ -349,10 +371,26 @@ 411 | printXMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); | ^~~~~~~~~~~~~~ | printTextAlign +utils/cextract.c: In function 'getLength': +utils/cextract.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | fgets (buffer, 1024, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +utils/cextract.c: In function 'readfile': +utils/cextract.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 41 | fgets (buffer, 1024, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +prolagan.c: In function 'readfile': +prolagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args] + 93 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mlagan.c: In function 'readfile': order.c: In function 'readfile': order.c:61:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 61 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ +mlagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args] + 93 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c: In function 'readSubstMatrix': order.c:145:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 145 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); @@ -363,39 +401,28 @@ order.c:150:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 150 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -prolagan.c: In function 'readfile': -prolagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args] - 93 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -anchors.c: In function 'anchors_getline': -anchors.c:232:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 232 | fgets(temp, 1024, infile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ +fchaos.c: In function 'readfile': +fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] + 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mlagan.c: In function 'main': prolagan.c: In function 'main': +mlagan.c:1071:5: warning: implicit declaration of function 'printXMFAAlign'; did you mean 'printFASTAAlign'? [-Wimplicit-function-declaration] + 1071 | printXMFAAlign(outfile, final); + | ^~~~~~~~~~~~~~ + | printFASTAAlign prolagan.c:1091:5: warning: implicit declaration of function 'printXMFAAlign'; did you mean 'printFASTAAlign'? [-Wimplicit-function-declaration] 1091 | printXMFAAlign(outfile, final); | ^~~~~~~~~~~~~~ | printFASTAAlign +mlagan.c: In function 'readfile': +mlagan.c:79:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 79 | fgets(temp, 255, input); + | ^~~~~~~~~~~~~~~~~~~~~~~ prolagan.c: In function 'readfile': prolagan.c:79:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 79 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ -fchaos.c: In function 'readfile': -fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] - 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -utils/cextract.c: In function 'getLength': -utils/cextract.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | fgets (buffer, 1024, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -utils/cextract.c: In function 'readfile': -utils/cextract.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 41 | fgets (buffer, 1024, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -mlagan.c: In function 'readfile': -mlagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args] - 93 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:344:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 344 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ @@ -409,15 +436,6 @@ fchaos.c:628:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 628 | fscanf (file, "%d", &gappenext); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mlagan.c: In function 'main': -mlagan.c:1071:5: warning: implicit declaration of function 'printXMFAAlign'; did you mean 'printFASTAAlign'? [-Wimplicit-function-declaration] - 1071 | printXMFAAlign(outfile, final); - | ^~~~~~~~~~~~~~ - | printFASTAAlign -mlagan.c: In function 'readfile': -mlagan.c:79:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 79 | fgets(temp, 255, input); - | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cstat utils/cstat.c -Wl,-z,relro utils/cstat.c: In function 'cntlets': utils/cstat.c:51:10: warning: implicit declaration of function 'isspace' [-Wimplicit-function-declaration] @@ -439,6 +457,7 @@ 67 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/contigorder utils/contigorder.c -Wl,-z,relro +gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getbounds utils/getbounds.c -Wl,-z,relro skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); @@ -446,7 +465,6 @@ | | | | unsigned int void * | %p -gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getbounds utils/getbounds.c -Wl,-z,relro utils/contigorder.c: In function 'getFileInfo': utils/contigorder.c:15:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] 15 | fprintf (stderr, "contigorder: Error opening file: %s\n"); @@ -496,18 +514,16 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getoverlap utils/getoverlap.c -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/rc utils/rc.c -Wl,-z,relro -gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/seqmerge utils/seqmerge.c -Wl,-z,relro utils/rc.c: In function 'main': utils/rc.c:39:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | fgets(temp, 255, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/seqmerge utils/seqmerge.c -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorealign utils/scorealign.c -lm -Wl,-z,relro utils/seqmerge.c: In function 'main': utils/seqmerge.c:19:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorecontigs utils/scorecontigs.c -lm -Wl,-z,relro -gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getcontigpos utils/getcontigpos.c -Wl,-z,relro utils/scorealign.c: In function 'getSequence': utils/scorealign.c:266:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 266 | fgets (line, 1024, file); @@ -525,6 +541,8 @@ utils/scorealign.c:430:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 430 | fscanf (file, "%d%d", &gapopen, &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorecontigs utils/scorecontigs.c -lm -Wl,-z,relro +gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getcontigpos utils/getcontigpos.c -Wl,-z,relro utils/scorecontigs.c: In function 'cntlets': utils/scorecontigs.c:63:10: warning: implicit declaration of function 'isspace' [-Wimplicit-function-declaration] 63 | if (!isspace(currchar)) { @@ -573,18 +591,6 @@ 55 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/Glue utils/Glue.cpp -Wl,-z,relro -g++ -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/dotplot utils/dotplot.cpp -Wl,-z,relro -utils/dotplot.cpp: In function 'int main(int, char**)': -utils/dotplot.cpp:37:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 37 | fgets (buffer, 105, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~ -utils/dotplot.cpp:74:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 74 | fgets (buffer, 105, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~ -utils/dotplot.cpp:97:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 97 | fgets (buffer, 105, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -Wl,-z,relro multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ @@ -609,6 +615,16 @@ multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ +multial.c: In function 'readSubstMatrix': +multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 478 | fscanf (file, "%d", &k); + | ^~~~~~~~~~~~~~~~~~~~~~~ +multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 486 | fscanf (file, "%d", &gapstart); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 487 | fscanf (file, "%d", &gapcont); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ @@ -633,6 +649,7 @@ multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/dotplot utils/dotplot.cpp -Wl,-z,relro multial.c: In function 'readSubstMatrix': multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 478 | fscanf (file, "%d", &k); @@ -643,16 +660,17 @@ multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multial.c: In function 'readSubstMatrix': -multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 478 | fscanf (file, "%d", &k); - | ^~~~~~~~~~~~~~~~~~~~~~~ -multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 486 | fscanf (file, "%d", &gapstart); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 487 | fscanf (file, "%d", &gapcont); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +utils/dotplot.cpp: In function 'int main(int, char**)': +utils/dotplot.cpp:37:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 37 | fgets (buffer, 105, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~ +utils/dotplot.cpp:74:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 74 | fgets (buffer, 105, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~ +utils/dotplot.cpp:97:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 97 | fgets (buffer, 105, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -Wl,-z,relro utils/overlay.c: In function 'read_align': utils/overlay.c:119:10: warning: implicit declaration of function 'isspace' [-Wimplicit-function-declaration] 119 | if (!isspace(currchar)) { @@ -668,6 +686,13 @@ utils/overlay.c:109:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 109 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ +skiplist.c: In function 'printSLE': +skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] + 12 | printf(" %d %x\n", tbp->index, tbp->myelem); + | ~^ ~~~~~~~~~~~ + | | | + | unsigned int void * + | %p utils/Glue.cpp: In function 'void calculateScoreMatrix(int)': utils/Glue.cpp:64:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 64 | char *alpha = "ATCG"; @@ -678,13 +703,6 @@ utils/Glue.cpp:72:22: note: in expansion of macro 'NUCLEOTIDE_MATRIX_FILE' 72 | readScoreMatrix (NUCLEOTIDE_MATRIX_FILE); | ^~~~~~~~~~~~~~~~~~~~~~ -skiplist.c: In function 'printSLE': -skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] - 12 | printf(" %d %x\n", tbp->index, tbp->myelem); - | ~^ ~~~~~~~~~~~ - | | | - | unsigned int void * - | %p utils/Glue.cpp: In function 'void readScoreMatrix(char*)': utils/Glue.cpp:44:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 44 | fgets (line, 1024, file); @@ -699,13 +717,13 @@ 59 | fscanf (file, "%d%d", &gapopen, &gapcont); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function 'printSLE': +skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p -skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ @@ -778,12 +796,14 @@ 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/30597/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30597/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/30179 and its subdirectories -I: Current time: Thu Apr 13 09:53:47 -12 2023 -I: pbuilder-time-stamp: 1681422827 +I: removing directory /srv/workspace/pbuilder/30597 and its subdirectories +I: Current time: Thu May 16 18:17:48 +14 2024 +I: pbuilder-time-stamp: 1715833068