Diff of the two buildlogs: -- --- b1/build.log 2020-08-08 16:19:38.135118856 +0000 +++ b2/build.log 2020-08-08 16:25:27.800304633 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Sep 10 10:42:03 -12 2021 -I: pbuilder-time-stamp: 1631313723 +I: Current time: Sun Aug 9 06:19:55 +14 2020 +I: pbuilder-time-stamp: 1596903595 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 Tue Oct 9 03:29:01 2018 -12 +gpgv: Signature made Wed Oct 10 05:29:01 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -28,138 +28,172 @@ dpkg-source: info: unpacking sortmerna_2.1-3.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/38282/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/10606/tmp/hooks/D01_modify_environment starting +debug: Running on profitbricks-build12-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/10606/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/10606/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=18' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='3ec01010e0e047a19a2263f1222746f3' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='38282' - PS1='# ' - PS2='> ' + INVOCATION_ID=f32d88f3ed3346fd9bfb2e75173209d5 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-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=10606 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/tmp.VSYWMo5vIc/pbuilderrc_lOaN --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.VSYWMo5vIc/b1 --logfile b1/build.log sortmerna_2.1-3.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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/tmp.VSYWMo5vIc/pbuilderrc_JElc --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.VSYWMo5vIc/b2 --logfile b2/build.log sortmerna_2.1-3.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux profitbricks-build6-i386 4.19.0-10-amd64 #1 SMP Debian 4.19.132-1 (2020-07-24) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-10-686-pae #1 SMP Debian 4.19.132-1 (2020-07-24) i686 GNU/Linux I: ls -l /bin - total 5476 - -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 38692 Feb 28 2019 cat - -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown - -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp - -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash - -rwxr-xr-x 1 root root 120676 Feb 28 2019 date - -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd - -rwxr-xr-x 1 root root 100620 Feb 28 2019 df - -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir - -rwxr-xr-x 1 root root 79412 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 34532 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 34532 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 30112 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 206392 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 100952 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln - -rwxr-xr-x 1 root root 55400 Jul 26 2018 login - -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls - -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 42348 Jan 9 2019 more - -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount - -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 157832 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38660 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm - -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Sep 9 02:47 sh -> dash - -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty - -rwsr-xr-x 1 root root 71072 Jan 9 2019 su - -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync - -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar - -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch - -rwxr-xr-x 1 root root 34532 Feb 28 2019 true - -rwxr-xr-x 1 root root 17768 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount - -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34208 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/38282/tmp/hooks/D02_print_environment finished + total 5484 + -rwxr-xr-x 1 root root 1302248 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 38692 Mar 1 2019 cat + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 63268 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chown + -rwxr-xr-x 1 root root 153732 Mar 1 2019 cp + -rwxr-xr-x 1 root root 132820 Jan 18 2019 dash + -rwxr-xr-x 1 root root 120676 Mar 1 2019 date + -rwxr-xr-x 1 root root 92040 Mar 1 2019 dd + -rwxr-xr-x 1 root root 100620 Mar 1 2019 df + -rwxr-xr-x 1 root root 149736 Mar 1 2019 dir + -rwxr-xr-x 1 root root 79412 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 34532 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 34532 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 67700 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 30112 Apr 23 09:38 fusermount + -rwxr-xr-x 1 root root 206392 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 100952 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 21916 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 79752 Mar 1 2019 ln + -rwxr-xr-x 1 root root 55400 Jul 27 2018 login + -rwxr-xr-x 1 root root 149736 Mar 1 2019 ls + -rwxr-xr-x 1 root root 112032 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 87972 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 79748 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 46916 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 42348 Jan 10 2019 more + -rwsr-xr-x 1 root root 50592 Jan 10 2019 mount + -rwxr-xr-x 1 root root 13724 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 157832 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38660 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 46852 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 75588 Mar 1 2019 rm + -rwxr-xr-x 1 root root 42756 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 22276 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 9 06:23 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 8 22:26 sh.distrib -> dash + -rwxr-xr-x 1 root root 34532 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 79652 Mar 1 2019 stty + -rwsr-xr-x 1 root root 71072 Jan 10 2019 su + -rwxr-xr-x 1 root root 34564 Mar 1 2019 sync + -rwxr-xr-x 1 root root 504024 Apr 24 2019 tar + -rwxr-xr-x 1 root root 13860 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 104292 Mar 1 2019 touch + -rwxr-xr-x 1 root root 34532 Mar 1 2019 true + -rwxr-xr-x 1 root root 17768 Apr 23 09:38 ulockmgr_server + -rwsr-xr-x 1 root root 30108 Jan 10 2019 umount + -rwxr-xr-x 1 root root 34532 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 149736 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34208 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/10606/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -228,7 +262,7 @@ Get: 31 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] -Fetched 19.4 MB in 0s (78.9 MB/s) +Fetched 19.4 MB in 12s (1664 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 ... 19234 files and directories currently installed.) @@ -383,7 +417,7 @@ 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/sortmerna-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/sortmerna-2.1/ && 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 sortmerna dpkg-buildpackage: info: source version 2.1-3 dpkg-buildpackage: info: source distribution unstable @@ -468,7 +502,7 @@ make[1]: Entering directory '/build/sortmerna-2.1' touch index/.tobuild dh_auto_build - make -j18 + make -j10 make[2]: Entering directory '/build/sortmerna-2.1' gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/bdz.o cmph/bdz.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/bdz_ph.o cmph/bdz_ph.c @@ -505,12 +539,25 @@ g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/njn_random.o alp/njn_random.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/bitvector.o src/bitvector.cpp -gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o src/ssw.o src/ssw.c -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/outputformats.o src/outputformats.cpp +In file included from alp/njn_matrix.hpp:43, + from alp/njn_localmaxstatutil.hpp:39, + from alp/njn_localmaxstatutil.cpp:37: +alp/njn_vector.hpp: In member function 'virtual void Njn::Vector::free2()': +alp/njn_vector.hpp:334:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; + ^~ +alp/njn_vector.hpp:334:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; + ^~~~~~~~~~ +In file included from alp/njn_localmaxstatutil.hpp:39, + from alp/njn_localmaxstatutil.cpp:37: +alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix::free2()': +alp/njn_matrix.hpp:598:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; + ^~ +alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; + ^~~~~~~~~~ In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstatmatrix.cpp:37: @@ -530,10 +577,9 @@ alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/paralleltraversal.o src/paralleltraversal.cpp In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, - from alp/njn_localmaxstatutil.cpp:37: + from alp/njn_localmaxstat.cpp:42: alp/njn_vector.hpp: In member function 'virtual void Njn::Vector::free2()': alp/njn_vector.hpp:334:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; @@ -542,7 +588,7 @@ if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; ^~~~~~~~~~ In file included from alp/njn_localmaxstatutil.hpp:39, - from alp/njn_localmaxstatutil.cpp:37: + from alp/njn_localmaxstat.cpp:42: alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix::free2()': alp/njn_matrix.hpp:598:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; @@ -550,7 +596,36 @@ alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/main.o src/main.cpp +In file included from alp/njn_localmaxstat.cpp:36: +alp/sls_alp_data.hpp: At global scope: +alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] + static double dbl_max_log=log(DBL_MAX); + ^~~~~~~~~~~ +alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] + static long int small_long=(long int)((double)LONG_MIN/2.0); + ^~~~~~~~~~ +In file included from alp/sls_pvalues.hpp:43, + from alp/gumbel_params.hpp:42, + from alp/sls_alp_data.hpp:69, + from alp/njn_localmaxstat.cpp:36: +alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] + static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from alp/njn_localmaxstatutil.cpp:44: +alp/sls_alp_data.hpp: At global scope: +alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] + static double dbl_max_log=log(DBL_MAX); + ^~~~~~~~~~~ +alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] + static long int small_long=(long int)((double)LONG_MIN/2.0); + ^~~~~~~~~~ +In file included from alp/sls_pvalues.hpp:43, + from alp/gumbel_params.hpp:42, + from alp/sls_alp_data.hpp:69, + from alp/njn_localmaxstatutil.cpp:44: +alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] + static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/gumbel_params.cpp:45: @@ -570,6 +645,8 @@ alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp src/indexdb.cpp: In function 'int main(int, char**)': src/indexdb.cpp:1545:24: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] fprintf(stderr,"\n check sequence # %ld\n\n",strs); @@ -592,26 +669,8 @@ src/indexdb.cpp:2074:39: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] for ( int shift = 0; shift < interval; shift++ ) ~~~~~~^~~~~~~~~~ -In file included from alp/njn_matrix.hpp:43, - from alp/njn_localmaxstatutil.hpp:39, - from alp/njn_localmaxstat.cpp:42: -alp/njn_vector.hpp: In member function 'virtual void Njn::Vector::free2()': -alp/njn_vector.hpp:334:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; - ^~ -alp/njn_vector.hpp:334:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; - ^~~~~~~~~~ -In file included from alp/njn_localmaxstatutil.hpp:39, - from alp/njn_localmaxstat.cpp:42: -alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix::free2()': -alp/njn_matrix.hpp:598:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; - ^~ -alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; - ^~~~~~~~~~ -In file included from alp/njn_localmaxstat.cpp:36: +In file included from alp/sls_alp.hpp:47, + from alp/gumbel_params.cpp:40: alp/sls_alp_data.hpp: At global scope: alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] static double dbl_max_log=log(DBL_MAX); @@ -622,13 +681,26 @@ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, - from alp/njn_localmaxstat.cpp:36: + from alp/sls_alp.hpp:47, + from alp/gumbel_params.cpp:40: alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp In file included from alp/sls_alp.hpp:47, - from alp/gumbel_params.cpp:40: -alp/sls_alp_data.hpp: At global scope: + from alp/sls_alp.cpp:37: +alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] + static double dbl_max_log=log(DBL_MAX); + ^~~~~~~~~~~ +In file included from alp/sls_pvalues.hpp:43, + from alp/gumbel_params.hpp:42, + from alp/sls_alp_data.hpp:69, + from alp/sls_alp.hpp:47, + from alp/sls_alp.cpp:37: +alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] + static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from alp/sls_alp_data.cpp:37: alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] static double dbl_max_log=log(DBL_MAX); ^~~~~~~~~~~ @@ -638,13 +710,21 @@ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, - from alp/sls_alp.hpp:47, - from alp/gumbel_params.cpp:40: + from alp/sls_alp_data.cpp:37: alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from alp/njn_localmaxstatutil.cpp:44: -alp/sls_alp_data.hpp: At global scope: +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/bitvector.o src/bitvector.cpp +gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o src/ssw.o src/ssw.c +In file included from alp/sls_pvalues.cpp:37: +alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] + static double dbl_max_log=log(DBL_MAX); + ^~~~~~~~~~~ +alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] + static long int small_long=(long int)((double)LONG_MIN/2.0); + ^~~~~~~~~~ +In file included from alp/sls_alp_regression.hpp:47, + from alp/sls_alp_regression.cpp:37: alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] static double dbl_max_log=log(DBL_MAX); ^~~~~~~~~~~ @@ -654,10 +734,26 @@ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, - from alp/njn_localmaxstatutil.cpp:44: + from alp/sls_alp_regression.hpp:47, + from alp/sls_alp_regression.cpp:37: +alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] + static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from alp/sls_alp_sim.hpp:48, + from alp/sls_alp_sim.cpp:37: +alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] + static long int small_long=(long int)((double)LONG_MIN/2.0); + ^~~~~~~~~~ +In file included from alp/sls_pvalues.hpp:43, + from alp/gumbel_params.hpp:42, + from alp/sls_alp_data.hpp:69, + from alp/sls_alp_sim.hpp:48, + from alp/sls_alp_sim.cpp:37: alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/outputformats.o src/outputformats.cpp +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/paralleltraversal.o src/paralleltraversal.cpp src/outputformats.cpp: In function 'void report_blast(std::ofstream&, s_align*, char*, char*, char*, char*, char*, double, uint32_t, uint32_t, bool, double, double, uint32_t, uint32_t)': src/outputformats.cpp:176:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int l = 0; l < user_opts.size(); l++ ) @@ -700,89 +796,11 @@ src/outputformats.cpp:692:30: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] if ( (i+2) < strs) end_read = reads[i+1]; ~~~~~~^~~~~~ -In file included from alp/sls_alp_data.cpp:37: -alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] - static double dbl_max_log=log(DBL_MAX); - ^~~~~~~~~~~ -alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] - static long int small_long=(long int)((double)LONG_MIN/2.0); - ^~~~~~~~~~ -In file included from alp/sls_pvalues.hpp:43, - from alp/gumbel_params.hpp:42, - from alp/sls_alp_data.hpp:69, - from alp/sls_alp_data.cpp:37: -alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] - static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from alp/sls_alp.hpp:47, - from alp/sls_alp.cpp:37: -alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] - static double dbl_max_log=log(DBL_MAX); - ^~~~~~~~~~~ -In file included from alp/sls_pvalues.hpp:43, - from alp/gumbel_params.hpp:42, - from alp/sls_alp_data.hpp:69, - from alp/sls_alp.hpp:47, - from alp/sls_alp.cpp:37: -alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] - static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from alp/sls_alp_regression.hpp:47, - from alp/sls_alp_regression.cpp:37: -alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] - static double dbl_max_log=log(DBL_MAX); - ^~~~~~~~~~~ -alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] - static long int small_long=(long int)((double)LONG_MIN/2.0); - ^~~~~~~~~~ -In file included from alp/sls_pvalues.hpp:43, - from alp/gumbel_params.hpp:42, - from alp/sls_alp_data.hpp:69, - from alp/sls_alp_regression.hpp:47, - from alp/sls_alp_regression.cpp:37: -alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] - static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from alp/sls_pvalues.cpp:37: -alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] - static double dbl_max_log=log(DBL_MAX); - ^~~~~~~~~~~ -alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] - static long int small_long=(long int)((double)LONG_MIN/2.0); - ^~~~~~~~~~ -In file included from alp/sls_alp_sim.hpp:48, - from alp/sls_alp_sim.cpp:37: -alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] - static long int small_long=(long int)((double)LONG_MIN/2.0); - ^~~~~~~~~~ -In file included from alp/sls_pvalues.hpp:43, - from alp/gumbel_params.hpp:42, - from alp/sls_alp_data.hpp:69, - from alp/sls_alp_sim.hpp:48, - from alp/sls_alp_sim.cpp:37: -alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] - static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/main.o src/main.cpp src/paralleltraversal.cpp: In function 'void traversetrie_align(NodeElement*, uint32_t, unsigned char, unsigned char*, unsigned char*, bool&, std::vector&, uint32_t, uint32_t, uint32_t)': src/paralleltraversal.cpp:387:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for ( int f = 0; f < id_hits.size(); f++ ) ~~^~~~~~~~~~~~~~~~ -In file included from src/../include/paralleltraversal.hpp:36, - from src/main.cpp:26: -src/../include/../alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] - static double dbl_max_log=log(DBL_MAX); - ^~~~~~~~~~~ -src/../include/../alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] - static long int small_long=(long int)((double)LONG_MIN/2.0); - ^~~~~~~~~~ -In file included from src/../include/../alp/sls_pvalues.hpp:43, - from src/../include/../alp/gumbel_params.hpp:42, - from src/../include/../alp/sls_alp_data.hpp:69, - from src/../include/paralleltraversal.hpp:36, - from src/main.cpp:26: -src/../include/../alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] - static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/paralleltraversal.cpp: In function 'void load_index(char*, std::__cxx11::string, kmer*&, kmer_origin*&, uint32_t&, uint32_t)': src/paralleltraversal.cpp:1005:29: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((NodeElement *&) dst)+=4; @@ -835,6 +853,22 @@ src/../include/../alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from src/../include/paralleltraversal.hpp:36, + from src/main.cpp:26: +src/../include/../alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] + static double dbl_max_log=log(DBL_MAX); + ^~~~~~~~~~~ +src/../include/../alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] + static long int small_long=(long int)((double)LONG_MIN/2.0); + ^~~~~~~~~~ +In file included from src/../include/../alp/sls_pvalues.hpp:43, + from src/../include/../alp/gumbel_params.hpp:42, + from src/../include/../alp/sls_alp_data.hpp:69, + from src/../include/paralleltraversal.hpp:36, + from src/main.cpp:26: +src/../include/../alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] + static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -Wl,-z,relro -Wl,-z,now -o indexdb_rna ./cmph/bdz.o ./cmph/bdz_ph.o ./cmph/bmz.o ./cmph/bmz8.o ./cmph/brz.o ./cmph/buffer_entry.o ./cmph/buffer_manager.o ./cmph/chd.o ./cmph/chd_ph.o ./cmph/chm.o ./cmph/cmph.o ./cmph/cmph_structs.o ./cmph/compressed_rank.o ./cmph/compressed_seq.o ./cmph/fch.o ./cmph/fch_buckets.o ./cmph/graph.o ./cmph/hash.o ./cmph/jenkins_hash.o ./cmph/miller_rabin.o ./cmph/select.o ./cmph/vqueue.o ./cmph/vstack.o ./src/indexdb.o -lm src/paralleltraversal.cpp: In function 'void paralleltraversal(char*, char*, char*, int32_t, int32_t, int32_t, int32_t, int32_t, std::vector >&, int, char**, bool, std::vector, std::__cxx11::basic_string > >&, bool)': src/paralleltraversal.cpp:1278:8: warning: 'filesig' may be used uninitialized in this function [-Wmaybe-uninitialized] @@ -890,12 +924,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/10606/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/10606/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/38282 and its subdirectories -I: Current time: Fri Sep 10 10:42:37 -12 2021 -I: pbuilder-time-stamp: 1631313757 +I: removing directory /srv/workspace/pbuilder/10606 and its subdirectories +I: Current time: Sun Aug 9 06:25:27 +14 2020 +I: pbuilder-time-stamp: 1596903927