Diff of the two buildlogs: -- --- b1/build.log 2020-04-16 20:59:13.625365664 +0000 +++ b2/build.log 2020-04-16 21:06:12.593012162 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed May 19 15:21:46 -12 2021 -I: pbuilder-time-stamp: 1621480906 +I: Current time: Fri Apr 17 10:59:16 +14 2020 +I: pbuilder-time-stamp: 1587070756 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Mon Dec 3 20:20:38 2018 -12 +gpgv: Signature made Tue Dec 4 22:20:38 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -35,6 +35,18 @@ dpkg-source: info: applying hardening.patch I: using fakeroot in build. I: Installing the build-deps +I: user script /srv/workspace/pbuilder/1835/tmp/hooks/D01_modify_environment starting +debug: Running on profitbricks-build2-i386. +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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/1835/tmp/hooks/D01_modify_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -107,7 +119,7 @@ Get: 33 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main i386 libboost1.67-dev i386 1.67.0-13+deb10u1 [8388 kB] Get: 35 http://deb.debian.org/debian buster/main i386 libboost-dev i386 1.67.0.1 [3864 B] -Fetched 27.7 MB in 0s (87.2 MB/s) +Fetched 27.7 MB in 15s (1850 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19231 files and directories currently installed.) @@ -270,7 +282,7 @@ fakeroot is already the newest version (1.23-1). 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 +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 dpkg-buildpackage: info: source package lagan dpkg-buildpackage: info: source version 2.0-3 dpkg-buildpackage: info: source distribution unstable @@ -282,7 +294,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/lagan-2.0' dh_auto_clean - make -j18 clean + make -j10 clean make[2]: Entering directory '/build/lagan-2.0' rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay make -C src clean @@ -305,7 +317,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/lagan-2.0' dh_auto_build --sourcedirectory=src - cd src && make -j18 "INSTALL=install --strip-program=true" + cd src && make -j10 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/lagan-2.0/src' gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../anchors anchors.c skiplist.c -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG -Wl,-z,relro @@ -317,14 +329,6 @@ gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/cextract utils/cextract.c -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/cstat utils/cstat.c -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -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 -O3 -o ../utils/getbounds utils/getbounds.c -Wl,-z,relro -gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/getlength utils/getlength.c -Wl,-z,relro -gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -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 -O3 -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 -O3 -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 -O3 -o ../utils/scorealign utils/scorealign.c -lm -Wl,-z,relro -gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -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 -O3 -o ../utils/getcontigpos utils/getcontigpos.c -Wl,-z,relro utils/contigorder.c: In function 'getFileInfo': utils/contigorder.c:15:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] fprintf (stderr, "contigorder: Error opening file: %s\n"); @@ -339,16 +343,6 @@ utils/contigorder.c:52:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] fprintf (stderr, "contigorder: Error opening file: %s\n"); ~^ -utils/scorecontigs.c: In function 'cntlets': -utils/scorecontigs.c:63:10: warning: implicit declaration of function 'isspace' [-Wimplicit-function-declaration] - if (!isspace(currchar)) { - ^~~~~~~ -utils/scorecontigs.c:64:18: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] - currchar = toupper(currchar); - ^~~~~~~ -utils/scorecontigs.c:65:27: warning: implicit declaration of function 'isalpha' [-Wimplicit-function-declaration] - if (!lettersonly || isalpha (currchar)){ - ^~~~~~~ order.c: In function 'doAlign': order.c:409:5: warning: implicit declaration of function 'printMFAAlign'; did you mean 'printBinAlign'? [-Wimplicit-function-declaration] printMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); @@ -358,22 +352,25 @@ printXMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); ^~~~~~~~~~~~~~ printTextAlign -utils/scorecontigs.c: In function 'main': -utils/scorecontigs.c:384:38: warning: format '%s' expects argument of type 'char *', but argument 6 has type 'char (*)[1024]' [-Wformat=] - if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){ - ~^ ~~~~~~~~~~~~~~~~~~~~~~~ +utils/cstat.c: In function 'cntlets': +utils/cstat.c:51:10: warning: implicit declaration of function 'isspace' [-Wimplicit-function-declaration] + if (!isspace(currchar)) { + ^~~~~~~ +utils/cstat.c:52:18: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] + currchar = toupper(currchar); + ^~~~~~~ mlagan.c: In function 'readfile': mlagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args] fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fchaos.c: In function 'readfile': -fchaos.c:357:18: warning: too many arguments for format [-Wformat-extra-args] - fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c: In function 'readfile': prolagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args] fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fchaos.c: In function 'readfile': +fchaos.c:357:18: warning: too many arguments for format [-Wformat-extra-args] + fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mlagan.c: In function 'main': mlagan.c:1071:5: warning: implicit declaration of function 'printXMFAAlign'; did you mean 'printFASTAAlign'? [-Wimplicit-function-declaration] printXMFAAlign(outfile, final); @@ -384,13 +381,33 @@ printXMFAAlign(outfile, final); ^~~~~~~~~~~~~~ printFASTAAlign -utils/cstat.c: In function 'cntlets': -utils/cstat.c:51:10: warning: implicit declaration of function 'isspace' [-Wimplicit-function-declaration] +gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -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=] + printf(" %d %x\n", tbp->index, tbp->myelem); + ~^ ~~~~~~~~~~~ + %p +gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/getlength utils/getlength.c -Wl,-z,relro +gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -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 -O3 -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 -O3 -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 -O3 -o ../utils/scorealign utils/scorealign.c -lm -Wl,-z,relro +gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/scorecontigs utils/scorecontigs.c -lm -Wl,-z,relro +utils/scorecontigs.c: In function 'cntlets': +utils/scorecontigs.c:63:10: warning: implicit declaration of function 'isspace' [-Wimplicit-function-declaration] if (!isspace(currchar)) { ^~~~~~~ -utils/cstat.c:52:18: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] +utils/scorecontigs.c:64:18: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] currchar = toupper(currchar); ^~~~~~~ +utils/scorecontigs.c:65:27: warning: implicit declaration of function 'isalpha' [-Wimplicit-function-declaration] + if (!lettersonly || isalpha (currchar)){ + ^~~~~~~ +utils/scorecontigs.c: In function 'main': +utils/scorecontigs.c:384:38: warning: format '%s' expects argument of type 'char *', but argument 6 has type 'char (*)[1024]' [-Wformat=] + if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){ + ~^ ~~~~~~~~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/getcontigpos utils/getcontigpos.c -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/fa2xfa utils/fa2xfa.c -Wl,-z,relro g++ -g -O2 -ffile-prefix-map=/build/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -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 -O3 -o ../utils/dotplot utils/dotplot.cpp -Wl,-z,relro @@ -402,24 +419,6 @@ utils/overlay.c:120:19: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] checkchar = toupper(currchar); ^~~~~~~ -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=] - printf(" %d %x\n", tbp->index, tbp->myelem); - ~^ ~~~~~~~~~~~ - %p -utils/overlay.c:134:5: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(allseqs[target]->seqname, temp, strlen(temp)+1); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -utils/overlay.c:134:45: note: length computed here - strncpy(allseqs[target]->seqname, temp, strlen(temp)+1); - ^~~~~~~~~~~~ -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] - char *alpha = "ATCG"; - ^~~~~~ -utils/Glue.cpp:72:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - readScoreMatrix (NUCLEOTIDE_MATRIX_FILE); - ^ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | ^~~~~~~~ @@ -468,10 +467,23 @@ multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | ^~~~~~~~~~ +utils/overlay.c:134:5: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(allseqs[target]->seqname, temp, strlen(temp)+1); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +utils/overlay.c:134:45: note: length computed here + strncpy(allseqs[target]->seqname, temp, strlen(temp)+1); + ^~~~~~~~~~~~ filebuffer.c: In function 'FileRead': filebuffer.c:123:34: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ? ^~~~~~~ +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] + char *alpha = "ATCG"; + ^~~~~~ +utils/Glue.cpp:72:44: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 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=] printf(" %d %x\n", tbp->index, tbp->myelem); @@ -511,7 +523,7 @@ make[2]: Leaving directory '/build/lagan-2.0/src' make[1]: Leaving directory '/build/lagan-2.0' dh_auto_test - make -j18 test + make -j10 test make[1]: Entering directory '/build/lagan-2.0' make -C src make[2]: Entering directory '/build/lagan-2.0/src' @@ -562,12 +574,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/1835/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1835/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/29379 and its subdirectories -I: Current time: Wed May 19 15:22:11 -12 2021 -I: pbuilder-time-stamp: 1621480931 +I: removing directory /srv/workspace/pbuilder/1835 and its subdirectories +I: Current time: Fri Apr 17 11:06:11 +14 2020 +I: pbuilder-time-stamp: 1587071171