Diff of the two buildlogs: -- --- b1/build.log 2020-08-10 19:14:39.336000329 +0000 +++ b2/build.log 2020-08-10 19:31:22.172957874 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Sep 12 13:21:06 -12 2021 -I: pbuilder-time-stamp: 1631496066 +I: Current time: Tue Aug 11 09:14:48 +14 2020 +I: pbuilder-time-stamp: 1597086888 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 '/var/lib/jenkins/.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/17193/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1595/tmp/hooks/D01_modify_environment starting +debug: Running on codethink-sled10-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +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/1595/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1595/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges: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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='17193' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1595 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.Dg8Saxt7PD/pbuilderrc_qwQX --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Dg8Saxt7PD/b1 --logfile b1/build.log bedops_2.4.35+dfsg-1.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.Dg8Saxt7PD/pbuilderrc_su59 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Dg8Saxt7PD/b2 --logfile b2/build.log bedops_2.4.35+dfsg-1.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink-sled15-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 - -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash - -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 34808 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 34808 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14264 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 35576 Feb 28 2019 cat - -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown - -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp - -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash - -rwxr-xr-x 1 root root 97136 Feb 28 2019 date - -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93752 Feb 28 2019 df - -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir - -rwxr-xr-x 1 root root 75984 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 31368 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 27256 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34824 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 174304 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 89656 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln - -rwxr-xr-x 1 root root 52544 Jul 26 2018 login - -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 38840 Jan 9 2019 more - -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138736 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 35560 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm - -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Sep 11 02:48 sh -> dash - -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty - -rwsr-xr-x 1 root root 59424 Jan 9 2019 su - -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync - -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar - -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch - -rwxr-xr-x 1 root root 27256 Feb 28 2019 true - -rwxr-xr-x 1 root root 14264 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount - -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34824 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/17193/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1216928 Apr 18 2019 bash + -rwxr-xr-x 3 root root 34808 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 34808 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 34808 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14264 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 35576 Mar 1 2019 cat + -rwxr-xr-x 1 root root 60256 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 56096 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 64368 Mar 1 2019 chown + -rwxr-xr-x 1 root root 134632 Mar 1 2019 cp + -rwxr-xr-x 1 root root 129536 Jan 18 2019 dash + -rwxr-xr-x 1 root root 97136 Mar 1 2019 date + -rwxr-xr-x 1 root root 76736 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93752 Mar 1 2019 df + -rwxr-xr-x 1 root root 138848 Mar 1 2019 dir + -rwxr-xr-x 1 root root 75984 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 31368 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 27256 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68792 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34824 Apr 23 09:38 fusermount + -rwxr-xr-x 1 root root 174304 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 89656 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 18440 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 64472 Mar 1 2019 ln + -rwxr-xr-x 1 root root 52544 Jul 27 2018 login + -rwxr-xr-x 1 root root 138848 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108552 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 76840 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 64480 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 39736 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 38840 Jan 10 2019 more + -rwsr-xr-x 1 root root 47112 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14344 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138736 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 35560 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 43712 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68440 Mar 1 2019 rm + -rwxr-xr-x 1 root root 39624 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 19144 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 11 09:14 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 9 22:26 sh.distrib -> dash + -rwxr-xr-x 1 root root 31384 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 72480 Mar 1 2019 stty + -rwsr-xr-x 1 root root 59424 Jan 10 2019 su + -rwxr-xr-x 1 root root 31416 Mar 1 2019 sync + -rwxr-xr-x 1 root root 449416 Apr 24 2019 tar + -rwxr-xr-x 1 root root 10560 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 88968 Mar 1 2019 touch + -rwxr-xr-x 1 root root 27256 Mar 1 2019 true + -rwxr-xr-x 1 root root 14264 Apr 23 09:38 ulockmgr_server + -rwsr-xr-x 1 root root 30728 Jan 10 2019 umount + -rwxr-xr-x 1 root root 31384 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138848 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34824 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/1595/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 arm64 sphinx-common all 1.8.4-1 [500 kB] Get: 84 http://deb.debian.org/debian buster/main arm64 python3-sphinx all 1.8.4-1 [481 kB] Get: 85 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] -Fetched 41.8 MB in 5s (8674 kB/s) +Fetched 41.8 MB in 2s (20.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 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 @@ -709,39 +743,39 @@ make -C applications/bed/bedops/src -f Makefile clean make -C applications/bed/closestfeats/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/bedextract/src -f Makefile clean -make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/bedmap/src' -rm -rf objects_typical make -C applications/bed/starch/src -f Makefile clean +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/closestfeats/src' +rm -rf objects-typical +rm -rf objects_typical make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/bedops/src' +make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/bedmap/src' rm -rf objects_typical -rm -rf ../bin -make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/closestfeats/src' rm -rf objects_typical -rm -rf ../bin -rm -rf objects-typical 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/starch/src' +rm -rf ../lib rm -rf ../bin -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' rm -rf ../bin rm -f ../lib/libstarch_debug.a -make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/closestfeats/src' rm -rf objects -rm -rf ../bin make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/sort-bed/src' -rm -f ../lib/libstarch_gprof.a make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/bedextract/src' +rm -f ../lib/libstarch_gprof.a +rm -rf ../bin +rm -rf ../bin rm -rf *.so *~ rm -rf objects rm -rf ../bin +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/bedops/src' +rm -rf ../bin +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/starch/src' make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/conversion/src' rm -rf third-party/bzip2-1.0.6 @@ -766,10 +800,10 @@ make[2]: Entering directory '/build/bedops-2.4.35+dfsg' make[2]: warning: -j8 forced in submake: resetting jobserver mode. #bzcat | tar -x -C third-party +#bzcat | tar -x -C third-party #cd third-party/jansson-2.6 && ./configure --prefix=/build/bedops-2.4.35+dfsg/third-party/jansson-2.6 && make && make install && cd /build/bedops-2.4.35+dfsg && rm -f jansson && ln -sf jansson-2.6 third-party/jansson #bzcat | tar -x -C third-party #cd third-party/bzip2-1.0.6 && make libbz2.a && cd /build/bedops-2.4.35+dfsg && rm -f bzip2 && ln -sf bzip2-1.0.6 third-party/bzip2 -#bzcat | tar -x -C third-party #cd third-party/zlib-1.2.7 && ./configure --static && make && cd /build/bedops-2.4.35+dfsg && rm -f zlib && ln -sf zlib-1.2.7 third-party/zlib make build -f /build/bedops-2.4.35+dfsg/system.mk/Makefile.linux make[3]: Entering directory '/build/bedops-2.4.35+dfsg' @@ -777,30 +811,29 @@ 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[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[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/sort-bed/src' 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 -make -C applications/bed/conversion/src -f Makefile build +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 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/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 +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 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/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 +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 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/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/starchFileHelpers.c -o objects-typical/starchFileHelpers.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/unstarchHelpers.c -o objects/unstarchHelpers.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 -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 ../../../../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] @@ -816,7 +849,6 @@ ../../../../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 ../../../../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); @@ -836,11 +868,10 @@ ../../../../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/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/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/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 ../../../../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); @@ -848,6 +879,7 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:330:87: note: length computed here strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 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/starchHelpers.c:354:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, s, strlen(s) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ @@ -860,12 +892,77 @@ ../../../../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::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); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:330:87: note: length computed here + strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); + ~~~~~~^~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:354:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(*chr, s, strlen(s) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:354:48: note: length computed here + strncpy(*chr, s, strlen(s) + 1); + ~~~~~~^~~ +../../../../interfaces/src/data/starch/starchHelpers.c:456:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:456:77: note: length computed here + strncpy(*remainder, reinterpret_cast( buffer ), strlen(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 +../../../../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); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:856:97: note: length computed here + strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:893:28: 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: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_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); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:856:97: note: length computed here + strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:893:28: 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:893:98: note: length computed here + strncat(nonCoordLineBuf, 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); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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 ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/starchHelpers.c -o objects_typical/starchHelpers.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); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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/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=] @@ -886,6 +983,14 @@ ../../../../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::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); + ~~~~~~^~~~~~~~~~~~ +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)': ../../../../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); @@ -899,6 +1004,25 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:59: note: length computed here strncpy(iter->signature, signature, strlen(signature) + 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::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); @@ -912,18 +1036,43 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:893:98: 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/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=] +../../../../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:856:97: 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:893:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] +../../../../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:893:98: note: length computed here +../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here + strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 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::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)': @@ -933,6 +1082,10 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:1281:97: note: length computed here strncpy(prevChromosome, 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/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); @@ -971,30 +1124,6 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:456:77: note: length computed here strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ -../../../../interfaces/src/data/starch/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: 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: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:1281:97: note: length computed here - strncpy(prevChromosome, 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); @@ -1014,6 +1143,7 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:456:77: note: length computed here strncpy(*remainder, reinterpret_cast( buffer ), strlen(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_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); @@ -1027,6 +1157,8 @@ ../../../../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/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); @@ -1040,25 +1172,6 @@ ../../../../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_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); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:330:87: note: length computed here - strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - ~~~~~~^~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:354:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(*chr, s, strlen(s) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:354:48: note: length computed here - strncpy(*chr, s, strlen(s) + 1); - ~~~~~~^~~ -../../../../interfaces/src/data/starch/starchHelpers.c:456:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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_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); @@ -1072,21 +1185,6 @@ ../../../../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); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:856:97: note: length computed here - strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:893:28: 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: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_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); @@ -1107,21 +1205,26 @@ ../../../../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=] - 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_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); - ~~~~~~^~~~~~~~~~~~ -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); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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/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); @@ -1129,32 +1232,13 @@ ../../../../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_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=] +../../../../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:2204:97: note: length computed here +../../../../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: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_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); @@ -1162,6 +1246,29 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 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_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/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); @@ -1194,40 +1301,20 @@ ../../../../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_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/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=] +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); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:856:97: 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:893:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] +../../../../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:893:98: note: length computed here +../../../../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 -Wextra -pedantic -ansi -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/starchSha1Digest.c -o objects_typical/starchSha1Digest.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); @@ -1235,48 +1322,32 @@ ../../../../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); - ~~~~~~^~~~~~~~~~~~ -../../../../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::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/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:982:24: warning: comparison is always true due to limited range of data type [-Wtype-limits] } while (currC != EOF); ^ -../../../../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=] +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/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); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2204:97: note: length computed here +../../../../interfaces/src/data/starch/starchHelpers.c:856:97: 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=] +../../../../interfaces/src/data/starch/starchHelpers.c:893:28: 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 +../../../../interfaces/src/data/starch/starchHelpers.c:893:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 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 ))); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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); @@ -1290,8 +1361,28 @@ ../../../../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/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/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); + ~~~~~~^~~~~~~~~~~~ +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/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); @@ -1311,12 +1402,19 @@ ../../../../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 -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 '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_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/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); @@ -1330,7 +1428,18 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:52: note: length computed here strncpy(*cTime, streamCTime, strlen(streamCTime) + 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/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/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.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_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/unstarchHelpers.c -o objects_typical/unstarchHelpers.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 -pedantic -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/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); @@ -1344,6 +1453,7 @@ ../../../../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 ../../../../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); @@ -1364,21 +1474,44 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:59: note: length computed here strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~^~~~~~~~~~~ -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/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 -Wextra -pedantic -ansi -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); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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_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); @@ -1398,6 +1531,20 @@ ../../../../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 '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_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); @@ -1430,25 +1577,6 @@ ../../../../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); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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); @@ -1462,41 +1590,10 @@ ../../../../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 '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 )); - ^ -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); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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_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_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); @@ -1516,29 +1613,44 @@ ../../../../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/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 ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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 +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 '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_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:982:24: warning: comparison is always true due to limited range of data type [-Wtype-limits] } while (currC != EOF); ^ -../../../../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); - ~~~~~~^~~~~~~~~~~~~ -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 +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_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 +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../../../.. +../../../../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/starchBase64Coding.c -o objects/starchBase64Coding.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 +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 ../../../../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); @@ -1552,15 +1664,16 @@ ../../../../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 ))); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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-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 ../bin +cp starchcluster_gnuParallel.tcsh ../bin/starchcluster_gnuParallel-typical +mkdir -p ../bin +cp starchcluster_sge.tcsh ../bin/starchcluster_sge-typical +mkdir -p ../bin +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 -Wextra -pedantic -ansi -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); @@ -1580,44 +1693,8 @@ ../../../../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); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 ../../../../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); @@ -1631,58 +1708,17 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:52: note: length computed here strncpy(*cTime, streamCTime, strlen(streamCTime) + 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 ))); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers -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 -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 ../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/starchSha1Digest.c -o objects/starchSha1Digest.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 -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -mkdir -p objects -../../../../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 ))); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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../../../.. -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 -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 -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -mkdir -p ../bin -cp starchcluster_gnuParallel.tcsh ../bin/starchcluster_gnuParallel-typical -mkdir -p ../bin -cp starchcluster_sge.tcsh ../bin/starchcluster_sge-typical -mkdir -p ../bin -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 -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 CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers +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 +make -C applications/bed/conversion/src -f Makefile build +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 mkdir -p ../lib ar rcs ../lib/libstarch.a objects/starchConstants.o objects/unstarchHelpers.o objects/starchHelpers.o objects/starchMetadataHelpers.o objects/starchFileHelpers.o objects/starchSha1Digest.o objects/starchBase64Coding.o -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 ../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../../../.. -rm -rf objects -make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/conversion/src' -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 unstarch.c -o objects/unstarch.o -iquote../../../../interfaces/general-headers -iquote../../../.. 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 ), @@ -1717,7 +1753,35 @@ starch.c:188:89: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( bedReportProgressN )) != STARCH_EXIT_SUCCESS) ^ -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 +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*)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:1219:93: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + static_cast( getArchiveType() ), + ^ +../../../../interfaces/general-headers/data/starch/starchApi.hpp:1223:91: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + static_cast( getArchiveHeaderFlag() ), + ^ +../../../../interfaces/general-headers/data/starch/starchApi.hpp:1224:96: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + static_cast( getArchiveShowNewlineFlag() )); + ^ +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractAllData(const string&, FILE*)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:1989:102: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + static_cast( getArchiveHeaderFlag() )) != 0 ) { + ^ +../../../../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/starch.o -o ../bin/starch-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 unstarch.c -o objects/unstarch.o -iquote../../../../interfaces/general-headers -iquote../../../.. +SortDetails.cpp: In function 'ChromBedData* initializeChromBedData(char*, double*)': +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] + strncpy(chrom->chromName, chromBuf, chromBufLen); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SortDetails.cpp:249:25: note: length computed here + chromBufLen = strlen(chromBuf); // we know >= 1 + ~~~~~~^~~~~~~~~~ unstarch.c: In function 'int main(int, char**)': unstarch.c:373:113: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( metadataOffset ), @@ -1752,7 +1816,6 @@ unstarch.c:781:156: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( sizeof(starchRevision2HeaderBytes) ), ^ -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/starch.o -o ../bin/starch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now unstarch.c: In function 'void starch::UNSTARCH_printMetadataSha1Signature(unsigned char*)': unstarch.c:1287:85: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), @@ -1760,7 +1823,23 @@ unstarch.c:1289:57: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( sha1BufferLength )); ^ -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 +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); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SortDetails.cpp:1326:33: note: length computed here + chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1 + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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] + strncpy(chrom->chromName, chromBuf, chromBufLen); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SortDetails.cpp: In function 'int processData(const char**, unsigned int, double, char*, bool, bool)': +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/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 starchcat.c -o objects/starchcat.o -iquote../../../../interfaces/general-headers -iquote../../../.. starchcat.c:6672:5: warning: this use of "defined" may not be portable [-Wexpansion-to-defined] @@ -1769,7 +1848,6 @@ starchcat.c:6678:5: warning: this use of "defined" may not be portable [-Wexpansion-to-defined] #if CLANG_COMPILER ^~~~~~~~~~~~~~ -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 In file included from /usr/include/c++/8/cassert:44, from starchcat.c:33: starchcat.c: In function 'int main(int, char**)': @@ -1818,6 +1896,8 @@ starchcat.c:223:112: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] assert (STARCHCAT_freeMetadataJSONObjects( &metadataJSONs, static_cast( numRecords ) ) ); ^ +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../../../.. starchcat.c: In function 'int starch::STARCHCAT2_rewriteInputRecordToOutput(starch::Metadata**, const char*, starch::CompressionType, const char*, const MetadataRecord*, size_t*, starch::Boolean, starch::Boolean, Bed::LineCountType)': starchcat.c:1253:115: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] UNSTARCH_reverseTransformCoordinates( static_cast( t_lineIdx ), @@ -1912,9 +1992,6 @@ 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 -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*)': starchstrip.c:116:85: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), @@ -1923,32 +2000,6 @@ static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); ^ 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*)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:1219:93: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - static_cast( getArchiveType() ), - ^ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:1223:91: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - static_cast( getArchiveHeaderFlag() ), - ^ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:1224:96: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - static_cast( getArchiveShowNewlineFlag() )); - ^ -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractAllData(const string&, FILE*)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:1989:102: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - static_cast( getArchiveHeaderFlag() )) != 0 ) { - ^ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:2000:101: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - static_cast( getArchiveHeaderFlag() )) != 0 ) { - ^ -SortDetails.cpp: In function 'ChromBedData* initializeChromBedData(char*, double*)': -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] - strncpy(chrom->chromName, chromBuf, chromBufLen); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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=] @@ -1978,14 +2029,6 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ -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); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 ../../../../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); @@ -1993,10 +2036,9 @@ ../../../../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); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical 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: + 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); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2004,82 +2046,39 @@ ../../../../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); - ~~~~~~^~~~~~~~~~~~ -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 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: + inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1698:86: ../../../../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: 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::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: + 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:1744:40: ../../../../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: 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::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: + 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:1755:45: ../../../../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 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': +../../../../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 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] - strncpy(chrom->chromName, chromBuf, chromBufLen); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SortDetails.cpp: In function 'int processData(const char**, unsigned int, double, char*, bool, bool)': -SortDetails.cpp:249:25: note: length computed here - chromBufLen = strlen(chromBuf); // we know >= 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); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:4815:53: note: length computed here - strncpy(cTime, creationTimestamp, strlen(creationTimestamp) + 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); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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 '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: + inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1609:40: ../../../../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); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2088,8 +2087,8 @@ 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:1698:86: + 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); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2099,7 +2098,7 @@ ~~~~~~^~~~~ 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:1744:40: + inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1565:86: ../../../../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); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2107,9 +2106,25 @@ ../../../../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); + ~~~~~~^~~~~~~~~~~~ +../../../../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:1755:45: + 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); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2117,48 +2132,50 @@ ../../../../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); + ~~~~~~^~~~~~~~~~~~ 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:1609:40: + inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80: ../../../../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: 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 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1617:45: + 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 'int starch::Starch::extractLine(std::__cxx11::string&)': +../../../../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:1565:86: + inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80: ../../../../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: 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::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); - ~~~~~~^~~~~~~~~~~~ +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 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::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80: + 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); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2178,7 +2195,8 @@ ~~~~~~^~~~~ 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::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80: + 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); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2225,7 +2243,6 @@ ../../../../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); @@ -2233,8 +2250,6 @@ ../../../../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); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -rm -rf objects -make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/starch/src' 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=] @@ -2265,17 +2280,13 @@ ../../../../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 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: -../../../../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 constructor 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]': -../../../../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); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:4815:53: note: length computed here + strncpy(cTime, creationTimestamp, strlen(creationTimestamp) + 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*)', @@ -2313,6 +2324,29 @@ ../../../../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); + ~~~~~~^~~~~~~ +rm -rf objects +make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/conversion/src' +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 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 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: +../../../../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 constructor 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]': +../../../../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 'Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, @@ -2325,11 +2359,6 @@ ../../../../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*)': @@ -2369,6 +2398,7 @@ ../../../../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 ../../../../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); @@ -2376,6 +2406,8 @@ ../../../../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); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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::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=] @@ -2407,6 +2439,8 @@ 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' @@ -2732,54 +2766,54 @@ dh_perl dh_link dh_strip_nondeterminism -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_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/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/_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/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/_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/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_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/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/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/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/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/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_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/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/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/_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_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/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/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_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_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/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/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/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/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/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_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/_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/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_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_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_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/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/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/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/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/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/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/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/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_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_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/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/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_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_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/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/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/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/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_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/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/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_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/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/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/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/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/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_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/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/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_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/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/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/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/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/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/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/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/reference_bedmap_mapref_ref3_padded.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 @@ -2801,12 +2835,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/1595/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1595/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/17193 and its subdirectories -I: Current time: Sun Sep 12 13:37:34 -12 2021 -I: pbuilder-time-stamp: 1631497054 +I: removing directory /srv/workspace/pbuilder/1595 and its subdirectories +I: Current time: Tue Aug 11 09:31:19 +14 2020 +I: pbuilder-time-stamp: 1597087879