Diff of the two buildlogs: -- --- b1/build.log 2021-06-20 16:28:32.936319434 +0000 +++ b2/build.log 2021-06-20 16:44:38.951745614 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jul 23 10:36:44 -12 2022 -I: pbuilder-time-stamp: 1658615804 +I: Current time: Mon Jun 21 06:28:34 +14 2021 +I: pbuilder-time-stamp: 1624206514 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Wed May 23 03:54:16 2018 -12 +gpgv: Signature made Thu May 24 05:54:16 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,136 +30,170 @@ dpkg-source: info: applying hardening.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/24492/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/30497/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +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/30497/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/30497/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='b6bdfd616e464f69889295a91b0593b0' - 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='24492' - PS1='# ' - PS2='> ' + INVOCATION_ID=b2e908d7801b4230990f8f6ca3b99992 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=30497 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.qmQ5BaUeVm/pbuilderrc_ib7M --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.qmQ5BaUeVm/b1 --logfile b1/build.log bedops_2.4.35+dfsg-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - 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.qmQ5BaUeVm/pbuilderrc_AQUP --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.qmQ5BaUeVm/b2 --logfile b2/build.log bedops_2.4.35+dfsg-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + 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 ionos15-amd64 5.10.0-0.bpo.7-amd64 #1 SMP Debian 5.10.40-1~bpo10+1 (2021-06-04) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-1 (2021-06-10) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 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 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 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 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 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 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 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 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 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 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 10 02:46 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 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/24492/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 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 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 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 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 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 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 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 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 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 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jun 21 06:28 sh -> bash + lrwxrwxrwx 1 root root 4 Jun 7 22:23 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 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/30497/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -294,7 +328,7 @@ Get: 83 http://deb.debian.org/debian buster/main amd64 sphinx-common all 1.8.4-1 [500 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 python3-sphinx all 1.8.4-1 [481 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] -Fetched 42.9 MB in 1s (59.1 MB/s) +Fetched 42.9 MB in 1s (71.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) @@ -686,7 +720,7 @@ 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/bedops-2.4.35+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/bedops-2.4.35+dfsg/ && 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 bedops dpkg-buildpackage: info: source version 2.4.35+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -696,7 +730,7 @@ fakeroot debian/rules clean dh clean --with sphinxdoc dh_auto_clean - make -j16 clean + make -j15 clean make[1]: Entering directory '/build/bedops-2.4.35+dfsg' make clean -j 8 -f system.mk/Makefile.linux make[2]: Entering directory '/build/bedops-2.4.35+dfsg' @@ -711,39 +745,39 @@ make -C applications/bed/bedextract/src -f Makefile clean make -C applications/bed/starch/src -f Makefile clean rm -rf modules -make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/sort-bed/src' make -C applications/bed/conversion/src -f Makefile clean +make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/sort-bed/src' make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/bedmap/src' rm -rf objects_typical make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/bedops/src' rm -rf objects_typical -make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/closestfeats/src' -rm -rf objects_typical -rm -rf objects-typical -rm -rf ../bin make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/conversion/src' rm -rf ../bin make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/starch/src' rm -rf ../lib make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/bedextract/src' rm -rf objects_typical +make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/closestfeats/src' +rm -rf objects_typical rm -rf ../bin rm -rf ../bin +rm -rf objects-typical +rm -f ../lib/libstarch_debug.a rm -rf ../bin rm -rf objects -make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/bedmap/src' -make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/bedops/src' -make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/closestfeats/src' -make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/sort-bed/src' -rm -f ../lib/libstarch_debug.a rm -rf ../bin -rm -rf *.so *~ +make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/bedops/src' +make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/bedmap/src' rm -f ../lib/libstarch_gprof.a -rm -rf objects +rm -rf ../bin make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/bedextract/src' +rm -rf objects +rm -rf *.so *~ +make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/closestfeats/src' rm -rf ../bin -make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/conversion/src' +make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/sort-bed/src' make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/starch/src' +make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/conversion/src' rm -rf third-party/bzip2-1.0.6 rm -f third-party/bzip2 rm -rf third-party/jansson-2.6 @@ -760,7 +794,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j16 "INSTALL=install --strip-program=true" + make -j15 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bedops-2.4.35+dfsg' make -j 8 -f system.mk/Makefile.linux make[2]: Entering directory '/build/bedops-2.4.35+dfsg' @@ -777,28 +811,28 @@ make -C applications/bed/sort-bed/src -f Makefile build make -C applications/bed/bedops/src -f Makefile build make -C applications/bed/closestfeats/src -f Makefile build -make -C applications/bed/bedextract/src -f Makefile build make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/sort-bed/src' +make -C applications/bed/bedextract/src -f Makefile build make -C applications/bed/starch/src -f Makefile build make -C applications/bed/conversion/src -f Makefile build make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/bedmap/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers -mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects-typical/starchConstants.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/bedops/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers +mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects-typical/starchConstants.o -iquote../../../../interfaces/general-headers +make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/conversion/src' +mkdir -p ../bin && gcc -Wall -Wextra -pedantic -std=c99 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -O3 -iquote"/build/bedops-2.4.35+dfsg/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" convert2bed.c -o ../bin/convert2bed-typical -lpthread +make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/starch/src' +mkdir -p objects make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/closestfeats/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/bedextract/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers -make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/starch/src' -mkdir -p objects -make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/conversion/src' -mkdir -p ../bin && gcc -Wall -Wextra -pedantic -std=c99 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -O3 -iquote"/build/bedops-2.4.35+dfsg/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" convert2bed.c -o ../bin/convert2bed-typical -lpthread g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchConstants.c -o objects/starchConstants.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects +mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects/unstarchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'void starch::UNSTARCH_printMetadataSignature(const unsigned char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2094:85: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] @@ -814,8 +848,8 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2387:90: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); ^ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects-typical/starchHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); @@ -836,9 +870,9 @@ strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers @@ -861,10 +895,7 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:456:77: note: length computed here strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)': ../../../../interfaces/src/data/starch/starchHelpers.c:330:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); @@ -884,6 +915,10 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:456:77: note: length computed here strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)': @@ -899,7 +934,6 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:59: note: length computed here strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~^~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:856:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); @@ -933,29 +967,6 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:1281:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(recTokBuf, token, strlen(token) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:57: note: length computed here - strncpy(recTokBuf, token, strlen(token) + 1); - ~~~~~~^~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:65: note: length computed here - strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); - ~~~~~~^~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(recFilename, token, strlen(token) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:59: note: length computed here - strncpy(recFilename, token, strlen(token) + 1); - ~~~~~~^~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:2316:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:1281:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); @@ -982,6 +993,42 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:456:77: note: length computed here strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(recTokBuf, token, strlen(token) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:57: note: length computed here + strncpy(recTokBuf, token, strlen(token) + 1); + ~~~~~~^~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:65: note: length computed here + strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); + ~~~~~~^~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(recFilename, token, strlen(token) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:59: note: length computed here + strncpy(recFilename, token, strlen(token) + 1); + ~~~~~~^~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:2204:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:2204:97: note: length computed here + strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:2239:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here + strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2316:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)': ../../../../interfaces/src/data/starch/starchHelpers.c:330:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); @@ -1001,6 +1048,19 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:456:77: note: length computed here strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(*note, streamNote, strlen(streamNote) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:50: note: length computed here + strncpy(*note, streamNote, strlen(streamNote) + 1); + ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:52: note: length computed here + strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); + ~~~~~~^~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)': ../../../../interfaces/src/data/starch/starchHelpers.c:330:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); @@ -1020,32 +1080,6 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:456:77: note: length computed here strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(*note, streamNote, strlen(streamNote) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:50: note: length computed here - strncpy(*note, streamNote, strlen(streamNote) + 1); - ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:52: note: length computed here - strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); - ~~~~~~^~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': -../../../../interfaces/src/data/starch/starchHelpers.c:2204:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2204:97: note: length computed here - strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2239:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here - strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:2204:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); @@ -1059,8 +1093,6 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ -mkdir -p objects -g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchHelpers.c -o objects/starchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:856:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); @@ -1074,6 +1106,13 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:893:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)': +../../../../interfaces/src/data/starch/starchHelpers.c:1281:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:1281:97: note: length computed here + strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:856:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); @@ -1087,6 +1126,8 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:893:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ +mkdir -p objects +g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchHelpers.c -o objects/starchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:856:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); @@ -1107,13 +1148,20 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:1281:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)': -../../../../interfaces/src/data/starch/starchHelpers.c:1281:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:2204:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:1281:97: note: length computed here +../../../../interfaces/src/data/starch/starchHelpers.c:2204:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:2239:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here + strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~^~~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:1281:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); @@ -1121,20 +1169,13 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:1281:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': -../../../../interfaces/src/data/starch/starchHelpers.c:2204:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2204:97: note: length computed here +../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2239:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here - strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:2204:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); @@ -1148,19 +1189,13 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': -../../../../interfaces/src/data/starch/starchHelpers.c:2204:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2204:97: note: length computed here +../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2239:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here - strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)': ../../../../interfaces/src/data/starch/starchHelpers.c:330:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); @@ -1180,20 +1215,19 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:456:77: note: length computed here strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': -../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here - strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': -../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:2204:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here +../../../../interfaces/src/data/starch/starchHelpers.c:2204:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:2239:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here + strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); @@ -1226,20 +1260,7 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:893:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': -../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here - strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': -../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here - strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~^~~~~~~~~~~~ +mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects-typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); @@ -1259,7 +1280,6 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects-typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:2204:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); @@ -1273,9 +1293,13 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here + strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(iter->filename, fn, strlen(fn) + 1); @@ -1289,10 +1313,61 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:59: note: length computed here strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~^~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here + strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(recTokBuf, token, strlen(token) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:57: note: length computed here + strncpy(recTokBuf, token, strlen(token) + 1); + ~~~~~~^~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:65: note: length computed here + strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); + ~~~~~~^~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(recFilename, token, strlen(token) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:59: note: length computed here + strncpy(recFilename, token, strlen(token) + 1); + ~~~~~~^~~~~~~ +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(*note, streamNote, strlen(streamNote) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:50: note: length computed here + strncpy(*note, streamNote, strlen(streamNote) + 1); + ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:52: note: length computed here + strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); + ~~~~~~^~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2316:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here + strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~^~~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(iter->filename, fn, strlen(fn) + 1); @@ -1306,6 +1381,22 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:59: note: length computed here strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~^~~~~~~~~~~ +mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p ../bin && g++ -o ../bin/bedmap-typical -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedmap.cpp +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'void starch::UNSTARCH_printMetadataSignature(const unsigned char*)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2094:85: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), + ^ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2096:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + static_cast( mdSha1BufferLength )); + ^ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2385:105: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), + ^ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2387:90: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); + ^ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(iter->filename, fn, strlen(fn) + 1); @@ -1351,27 +1442,44 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:59: note: length computed here strncpy(recFilename, token, strlen(token) + 1); ~~~~~~^~~~~~~ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(recTokBuf, token, strlen(token) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:57: note: length computed here - strncpy(recTokBuf, token, strlen(token) + 1); - ~~~~~~^~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:65: note: length computed here - strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); - ~~~~~~^~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(recFilename, token, strlen(token) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:59: note: length computed here - strncpy(recFilename, token, strlen(token) + 1); - ~~~~~~^~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:83: note: length computed here + strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:75: note: length computed here + strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:75: note: length computed here + strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:83: note: length computed here + strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:75: note: length computed here + strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:75: note: length computed here + strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*note, streamNote, strlen(streamNote) + 1); @@ -1385,6 +1493,8 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:52: note: length computed here strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); ~~~~~~^~~~~~~~~~~~~ +mkdir -p objects +g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recTokBuf, token, strlen(token) + 1); @@ -1404,13 +1514,6 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:59: note: length computed here strncpy(recFilename, token, strlen(token) + 1); ~~~~~~^~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': -../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here - strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recTokBuf, token, strlen(token) + 1); @@ -1443,20 +1546,10 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:52: note: length computed here strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); ~~~~~~^~~~~~~~~~~~~ -mkdir -p ../bin && g++ -o ../bin/bedmap-typical -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedmap.cpp -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(*note, streamNote, strlen(streamNote) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:50: note: length computed here - strncpy(*note, streamNote, strlen(streamNote) + 1); - ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:52: note: length computed here - strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); - ~~~~~~^~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*note, streamNote, strlen(streamNote) + 1); @@ -1470,87 +1563,26 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:52: note: length computed here strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); ~~~~~~^~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:83: note: length computed here - strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:75: note: length computed here - strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:75: note: length computed here - strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'void starch::UNSTARCH_printMetadataSignature(const unsigned char*)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:2094:85: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), - ^ -../../../../interfaces/src/data/starch/unstarchHelpers.c:2096:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - static_cast( mdSha1BufferLength )); - ^ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:2385:105: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), - ^ -../../../../interfaces/src/data/starch/unstarchHelpers.c:2387:90: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); - ^ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects -g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:83: note: length computed here - strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:75: note: length computed here - strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:75: note: length computed here - strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:83: note: length computed here - strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:75: note: length computed here - strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:75: note: length computed here - strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(iter->filename, fn, strlen(fn) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:47: note: length computed here + strncpy(iter->filename, fn, strlen(fn) + 1); + ~~~~~~^~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(iter->signature, signature, strlen(signature) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:59: note: length computed here + strncpy(iter->signature, signature, strlen(signature) + 1); + ~~~~~~^~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); @@ -1570,36 +1602,6 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:75: note: length computed here strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(iter->filename, fn, strlen(fn) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:47: note: length computed here - strncpy(iter->filename, fn, strlen(fn) + 1); - ~~~~~~^~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(iter->signature, signature, strlen(signature) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:59: note: length computed here - strncpy(iter->signature, signature, strlen(signature) + 1); - ~~~~~~^~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:2316:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recTokBuf, token, strlen(token) + 1); @@ -1619,8 +1621,10 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:59: note: length computed here strncpy(recFilename, token, strlen(token) + 1); ~~~~~~^~~~~~~ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers -mkdir -p ../bin && g++ -o ../bin/bedextract-typical -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ExtractRows.cpp +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2316:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*note, streamNote, strlen(streamNote) + 1); @@ -1638,26 +1642,59 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2316:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:83: note: length computed here + strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:75: note: length computed here + strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:75: note: length computed here + strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects-typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p ../bin && g++ -o ../bin/closest-features-typical -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ClosestFeature.cpp +mkdir -p objects +g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects/starchFileHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2316:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects-typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers +mkdir -p objects +rm -rf objects +g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../.. +make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/conversion/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2316:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects -g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects/starchFileHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. -mkdir -p objects -g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../.. -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers -mkdir -p ../bin && g++ -o ../bin/bedops-typical -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedops.cpp +mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p objects g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects/starchBase64Coding.o -iquote../../../../interfaces/general-headers -iquote../../../.. -rm -rf objects -make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/conversion/src' +mkdir -p ../bin && g++ -o ../bin/bedops-typical -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedops.cpp +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers +mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers mkdir -p ../bin cp starchcluster_gnuParallel.tcsh ../bin/starchcluster_gnuParallel-typical mkdir -p ../bin @@ -1666,12 +1703,8 @@ cp starchcluster_slurm.tcsh ../bin/starchcluster_slurm-typical mkdir -p ../bin cp starch-diff.py ../bin/starch-diff-typical -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers -mkdir -p ../bin && g++ -o ../bin/closest-features-typical -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ClosestFeature.cpp mkdir -p ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical mkdir -p ../bin && cp update-sort-bed-starch-slurm.py ../bin/update-sort-bed-starch-slurm-typical mkdir -p ../bin && cp update-sort-bed-migrate-candidates.py ../bin/update-sort-bed-migrate-candidates-typical @@ -1681,6 +1714,7 @@ mkdir -p ../bin g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starch.c -o objects/starch.o -iquote../../../../interfaces/general-headers -iquote../../../.. g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c unstarch.c -o objects/unstarch.o -iquote../../../../interfaces/general-headers -iquote../../../.. +mkdir -p ../bin && g++ -o ../bin/bedextract-typical -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ExtractRows.cpp starch.c: In function 'int main(int, char**)': starch.c:97:81: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( type ), @@ -1907,6 +1941,7 @@ starchcat.c:6325:107: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] UNSTARCH_reverseTransformCoordinates( static_cast( *t_lineIdxPtr ), ^ +g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/unstarch.o -o ../bin/unstarch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::listJSONMetadata(FILE*, FILE*)': @@ -1926,7 +1961,6 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:2000:101: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( getArchiveHeaderFlag() )) != 0 ) { ^ -g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/unstarch.o -o ../bin/unstarch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now mkdir -p ../bin g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starchstrip.c -o objects/starchstrip.o -iquote../../../../interfaces/general-headers -iquote../../../.. starchstrip.c: In function 'void starch::STARCHSTRIP_write_updated_metadata(FILE*)': @@ -1943,6 +1977,7 @@ SortDetails.cpp:249:25: note: length computed here chromBufLen = strlen(chromBuf); // we know >= 1 ~~~~~~^~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchstrip.o -o ../bin/starchstrip-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now SortDetails.cpp: In function 'void lexSortBedData(BedData*)': SortDetails.cpp:1327:20: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(chromBuf, beds->chroms[i]->chromName, chromBufLen); @@ -1950,7 +1985,6 @@ SortDetails.cpp:1326:33: note: length computed here chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchstrip.o -o ../bin/starchstrip-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now In function 'ChromBedData* initializeChromBedData(char*, double*)', inlined from 'int processData(const char**, unsigned int, double, char*, bool, bool)' at SortDetails.cpp:909:59: SortDetails.cpp:250:12: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] @@ -1960,36 +1994,6 @@ SortDetails.cpp:249:25: note: length computed here chromBufLen = strlen(chromBuf); // we know >= 1 ~~~~~~^~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, - from ExtractRows.cpp:43: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - std::strncpy(_recTokBuf, _token, strlen(_token) + 1); - ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here - std::strncpy(_recTokBuf, _token, strlen(_token) + 1); - ~~~~~~^~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); - ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here - std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); - ~~~~~~~~~~~^~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - std::strncpy(_recFilename, _token, strlen(_token) + 1); - ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here - std::strncpy(_recFilename, _token, strlen(_token) + 1); - ~~~~~~^~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, - from ExtractRows.cpp:43: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'void starch::Starch::setCurrentChromosome(char*)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(currentChromosome, _cC, strlen(_cC) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here - strncpy(currentChromosome, _cC, strlen(_cC) + 1); - ~~~~~~^~~~~ starchcat.c: In function 'int starch::STARCHCAT_buildMetadataRecords(json_t***, starch::MetadataRecord**, unsigned int, int, const char**)': starchcat.c:4815:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(cTime, creationTimestamp, strlen(creationTimestamp) + 1); @@ -1997,32 +2001,13 @@ starchcat.c:4815:53: note: length computed here strncpy(cTime, creationTimestamp, strlen(creationTimestamp) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:118: note: length computed here - strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void starch::Starch::setCurrentChromosome(char*)', - inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:867:37, - inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1617:45: -../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(currentChromosome, _cC, strlen(_cC) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here - strncpy(currentChromosome, _cC, strlen(_cC) + 1); - ~~~~~~^~~~~ -In member function 'void starch::Starch::setCurrentRemainder(char*)', - inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1796:36: -../../../../interfaces/general-headers/data/starch/starchApi.hpp:892:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:892:61: note: length computed here - strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); - ~~~~~~^~~~~~~~~~~~ +starchcat.c: In function 'int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)': +starchcat.c:2892:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:2892:78: note: length computed here + strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); + ~~~~~~^~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); @@ -2032,38 +2017,6 @@ ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, - inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, - inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1445:22: -../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(currentChromosome, _cC, strlen(_cC) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here - strncpy(currentChromosome, _cC, strlen(_cC) + 1); - ~~~~~~^~~~~ -In member function 'void starch::Starch::setCurrentChromosome(char*)', - inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:867:37, - inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1465:37: -../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(currentChromosome, _cC, strlen(_cC) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here - strncpy(currentChromosome, _cC, strlen(_cC) + 1); - ~~~~~~^~~~~ -In member function 'void starch::Starch::setCurrentChromosome(char*)', - inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, - inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, - inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1500:22: -../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(currentChromosome, _cC, strlen(_cC) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here - strncpy(currentChromosome, _cC, strlen(_cC) + 1); - ~~~~~~^~~~~ -In member function 'void starch::Starch::setCurrentChromosome(char*)', - inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1514:82: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); @@ -2171,16 +2124,6 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ -starchcat.c: In function 'int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)': -starchcat.c:2892:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:2892:78: note: length computed here - strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); - ~~~~~~^~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchcat.o -o ../bin/starchcat-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now -rm -rf objects -make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/starch/src' In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': @@ -2220,6 +2163,76 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ +g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchcat.o -o ../bin/starchcat-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:118: note: length computed here + strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void starch::Starch::setCurrentRemainder(char*)', + inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1796:36: +../../../../interfaces/general-headers/data/starch/starchApi.hpp:892:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:892:61: note: length computed here + strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); + ~~~~~~^~~~~~~~~~~~ +rm -rf objects +make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/starch/src' +In member function 'void starch::Starch::setCurrentChromosome(char*)', + inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, + inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, + inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1445:22: +../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(currentChromosome, _cC, strlen(_cC) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here + strncpy(currentChromosome, _cC, strlen(_cC) + 1); + ~~~~~~^~~~~ +In member function 'void starch::Starch::setCurrentChromosome(char*)', + inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:867:37, + inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1465:37: +../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(currentChromosome, _cC, strlen(_cC) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here + strncpy(currentChromosome, _cC, strlen(_cC) + 1); + ~~~~~~^~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, + from ExtractRows.cpp:43: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + std::strncpy(_recTokBuf, _token, strlen(_token) + 1); + ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here + std::strncpy(_recTokBuf, _token, strlen(_token) + 1); + ~~~~~~^~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); + ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here + std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); + ~~~~~~~~~~~^~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + std::strncpy(_recFilename, _token, strlen(_token) + 1); + ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here + std::strncpy(_recFilename, _token, strlen(_token) + 1); + ~~~~~~^~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, + from ExtractRows.cpp:43: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'void starch::Starch::setCurrentChromosome(char*)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(currentChromosome, _cC, strlen(_cC) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here + strncpy(currentChromosome, _cC, strlen(_cC) + 1); + ~~~~~~^~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); @@ -2227,6 +2240,16 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:118: note: length computed here strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void starch::Starch::setCurrentChromosome(char*)', + inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:867:37, + inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1617:45: +../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(currentChromosome, _cC, strlen(_cC) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here + strncpy(currentChromosome, _cC, strlen(_cC) + 1); + ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentRemainder(char*)', inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1796:36: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:892:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -2257,6 +2280,17 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ +In member function 'void starch::Starch::setCurrentChromosome(char*)', + inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, + inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, + inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1500:22: +../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(currentChromosome, _cC, strlen(_cC) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here + strncpy(currentChromosome, _cC, strlen(_cC) + 1); + ~~~~~~^~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)', @@ -2306,6 +2340,9 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ +mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now objects-typical/starchConstants.o objects-typical/starchFileHelpers.o objects-typical/starchHelpers.o objects-typical/starchMetadataHelpers.o objects-typical/unstarchHelpers.o objects-typical/starchSha1Digest.o objects-typical/starchBase64Coding.o objects-typical/SortDetails.o objects-typical/Sort.o objects-typical/CheckSort.o -ljansson -lz -lbz2 +rm -rf objects-typical +make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/sort-bed/src' In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, @@ -2317,11 +2354,6 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ -mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now objects-typical/starchConstants.o objects-typical/starchFileHelpers.o objects-typical/starchHelpers.o objects-typical/starchMetadataHelpers.o objects-typical/unstarchHelpers.o objects-typical/starchSha1Digest.o objects-typical/starchBase64Coding.o objects-typical/SortDetails.o objects-typical/Sort.o objects-typical/CheckSort.o -ljansson -lz -lbz2 -rm -rf objects-typical -make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/sort-bed/src' -rm -rf objects_typical -make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/bedextract/src' In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': @@ -2399,6 +2431,8 @@ strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ rm -rf objects_typical +make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/bedextract/src' +rm -rf objects_typical make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/closestfeats/src' rm -rf objects_typical make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/bedops/src' @@ -2468,7 +2502,7 @@ dh_testroot dh_prep dh_auto_install - make -j16 install DESTDIR=/build/bedops-2.4.35\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + make -j15 install DESTDIR=/build/bedops-2.4.35\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bedops-2.4.35+dfsg' mkdir -p bin cp applications/bed/conversion/src/wrappers/gvf2starch applications/bed/conversion/src/wrappers/bam2bed_gnuParallel applications/bed/conversion/src/wrappers/bam2starch_sge applications/bed/conversion/src/wrappers/bam2starch_slurm applications/bed/conversion/src/wrappers/psl2bed applications/bed/conversion/src/wrappers/gff2starch applications/bed/conversion/src/wrappers/wig2bed applications/bed/conversion/src/wrappers/sam2bed applications/bed/conversion/src/wrappers/psl2starch applications/bed/conversion/src/wrappers/rmsk2bed applications/bed/conversion/src/wrappers/vcf2bed applications/bed/conversion/src/wrappers/wig2starch applications/bed/conversion/src/wrappers/sam2starch applications/bed/conversion/src/wrappers/gtf2starch applications/bed/conversion/src/wrappers/rmsk2starch applications/bed/conversion/src/wrappers/bam2bed applications/bed/conversion/src/wrappers/vcf2starch applications/bed/conversion/src/wrappers/gff2bed applications/bed/conversion/src/wrappers/bam2bed_slurm applications/bed/conversion/src/wrappers/bam2starch_gnuParallel applications/bed/conversion/src/wrappers/bam2starch applications/bed/conversion/src/wrappers/gvf2bed applications/bed/conversion/src/wrappers/bam2bed_sge applications/bed/conversion/src/wrappers/gtf2bed bin @@ -2725,53 +2759,53 @@ dh_link dh_strip_nondeterminism debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_macosx_installer_screen_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_bedops_merge_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_metadatachecksum.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_magicbytes.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_starch_efficiency.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_metadatachecksum.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_notelementof_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_bedops_merge_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_inputs@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_intersect_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_stagger_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_mapref_ref1.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_stagger_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/SNP_DHS_matrix.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_static/logo_with_label_v3.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_notelementof_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_intersect_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_cygwin_installer_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/BEDOPS_Presentation_bedmap_ops.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_chromosomestreams.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_bedops_complement_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_padding.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_chromosomestreams.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_unstarch_extractiontime.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_complement_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_bedops_complement_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_everything@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_merge_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_mapref_ref2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/SNP_DHS_matrix_diseaseSorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_macosx_installer_icon.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_merge_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_complement_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_cygwin_installer_gcc_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/BEDOPS_Presentation_grok_tests.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_metadata.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_bedops_intersect_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedextract_mechanism.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_static/logo_with_label_v3.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_metadata.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_independent_grok.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_difference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_partition_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_bedops_intersect_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_elementof_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_inputs.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_mapref_ref3.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_inputs.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedextract_mechanism1.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_partition_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_difference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_cygwin_installer_git_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/BEDOPS_Presentation_starch_efficiency.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_metadataoffset.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_bedops_merge_unsorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedextract_nested_elements.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_macosx_installer_icon.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_metadataoffset.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_symmetricdifference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_chop_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_bedops_merge_unsorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_elementof_ba@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. -debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_mapref_all.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_mapref_ref3_padded.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_mapref_all.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/starchcluster_mechanism.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_chop_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_symmetricdifference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. dh_compress dh_fixperms dh_missing @@ -2785,20 +2819,22 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'bedops' in '../bedops_2.4.35+dfsg-1_amd64.deb'. -dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.35+dfsg-1_amd64.deb'. dpkg-deb: building package 'bedops-doc' in '../bedops-doc_2.4.35+dfsg-1_all.deb'. +dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.35+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bedops_2.4.35+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/30497/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30497/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/24492 and its subdirectories -I: Current time: Sat Jul 23 10:51:32 -12 2022 -I: pbuilder-time-stamp: 1658616692 +I: removing directory /srv/workspace/pbuilder/30497 and its subdirectories +I: Current time: Mon Jun 21 06:44:38 +14 2021 +I: pbuilder-time-stamp: 1624207478