Diff of the two buildlogs: -- --- b1/build.log 2021-07-28 17:22:11.888390130 +0000 +++ b2/build.log 2021-07-28 17:48:42.784726567 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jul 28 04:42:44 -12 2021 -I: pbuilder-time-stamp: 1627490564 +I: Current time: Thu Jul 29 07:22:21 +14 2021 +I: pbuilder-time-stamp: 1627492941 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./bedops_2.4.39+dfsg1-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.ORWOTl8N/trustedkeys.kbx': General error -gpgv: Signature made Fri Feb 19 01:34:11 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.q6eVx9Jq/trustedkeys.kbx': General error +gpgv: Signature made Sat Feb 20 03:34:11 2021 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -33,135 +33,169 @@ dpkg-source: info: applying parallel.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/28355/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/30359/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +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/30359/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/30359/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + 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]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='5ebf39bb3cc5465295603789ed7e8aa4' - 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='28355' - PS1='# ' - PS2='> ' + INVOCATION_ID=5cde1a765f1a4dcba20b9a9950c10886 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=30359 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.uMbyGqcxyT/pbuilderrc_O2q4 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.uMbyGqcxyT/b1 --logfile b1/build.log bedops_2.4.39+dfsg1-2.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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.uMbyGqcxyT/pbuilderrc_d7D4 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.uMbyGqcxyT/b2 --logfile b2/build.log --extrapackages usrmerge bedops_2.4.39+dfsg1-2.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux ff4a 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-2 (2021-07-20) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-arm64 #1 SMP Debian 5.10.46-2 (2021-07-20) aarch64 GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Jun 21 14:26 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Feb 7 02:38 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Feb 7 02:38 more - -rwsr-xr-x 1 root root 34400 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 9824 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 24 21:28 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Feb 7 02:38 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/28355/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Jun 22 16:26 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Feb 8 04:38 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Feb 8 04:38 more + -rwsr-xr-x 1 root root 34400 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 9824 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 29 07:22 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 25 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Feb 8 04:38 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/30359/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -296,7 +330,7 @@ Get: 81 http://deb.debian.org/debian bullseye/main armhf sphinx-common all 3.4.3-2 [578 kB] Get: 82 http://deb.debian.org/debian bullseye/main armhf python3-sphinx all 3.4.3-2 [545 kB] Get: 83 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB] -Fetched 41.3 MB in 6s (7244 kB/s) +Fetched 41.3 MB in 4s (10.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19398 files and directories currently installed.) @@ -672,9 +706,42 @@ Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). -0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main armhf libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (949 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 29389 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/bedops-2.4.39+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bedops_2.4.39+dfsg1-2_source.changes +hostname: Name or service not known +I: Running cd /build/bedops-2.4.39+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../bedops_2.4.39+dfsg1-2_source.changes dpkg-buildpackage: info: source package bedops dpkg-buildpackage: info: source version 2.4.39+dfsg1-2 dpkg-buildpackage: info: source distribution unstable @@ -686,7 +753,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/bedops-2.4.39+dfsg1' dh_auto_clean - make -j3 clean + make -j4 clean make[2]: Entering directory '/build/bedops-2.4.39+dfsg1' make clean -f system.mk/Makefile.linux make[3]: Entering directory '/build/bedops-2.4.39+dfsg1' @@ -697,38 +764,38 @@ rm -rf modules make -C applications/bed/sort-bed/src -f Makefile clean make -C applications/bed/bedops/src -f Makefile clean +make -C applications/bed/closestfeats/src -f Makefile clean make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/sort-bed/src' make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedmap/src' rm -rf objects_typical rm -rf ../bin make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedops/src' rm -rf objects_typical -rm -rf ../bin +make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/closestfeats/src' +rm -rf objects_typical make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedmap/src' -make -C applications/bed/closestfeats/src -f Makefile clean -make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedops/src' make -C applications/bed/bedextract/src -f Makefile clean rm -rf objects-typical rm -rf ../bin -make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/sort-bed/src' -make -C applications/bed/starch/src -f Makefile clean -make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedextract/src' -make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/closestfeats/src' -rm -rf objects_typical -rm -rf objects_typical rm -rf ../bin rm -rf ../bin -make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedextract/src' +make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedops/src' +make -C applications/bed/starch/src -f Makefile clean +make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/closestfeats/src' make -C applications/bed/conversion/src -f Makefile clean +make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/sort-bed/src' +make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedextract/src' +rm -rf objects_typical +make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/conversion/src' make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/starch/src' rm -rf ../lib -make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/closestfeats/src' -make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/conversion/src' rm -rf ../bin +rm -rf ../bin +make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedextract/src' rm -f ../lib/libstarch_debug.a rm -rf objects -rm -f ../lib/libstarch_gprof.a rm -rf *.so *~ +rm -f ../lib/libstarch_gprof.a rm -rf objects rm -rf ../bin make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/conversion/src' @@ -751,13 +818,13 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j3 "INSTALL=install --strip-program=true" + make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bedops-2.4.39+dfsg1' make -f system.mk/Makefile.linux make[2]: Entering directory '/build/bedops-2.4.39+dfsg1' #bzcat | tar -x -C third-party -#cd third-party/jansson-2.6 && ./configure --prefix=/build/bedops-2.4.39+dfsg1/third-party/jansson-2.6 && make && make install && cd /build/bedops-2.4.39+dfsg1 && rm -f jansson && ln -sf jansson-2.6 third-party/jansson #bzcat | tar -x -C third-party +#cd third-party/jansson-2.6 && ./configure --prefix=/build/bedops-2.4.39+dfsg1/third-party/jansson-2.6 && make && make install && cd /build/bedops-2.4.39+dfsg1 && rm -f jansson && ln -sf jansson-2.6 third-party/jansson #cd third-party/bzip2-1.0.6 && make libbz2.a && cd /build/bedops-2.4.39+dfsg1 && 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-2.4.39+dfsg1 && rm -f zlib && ln -sf zlib-1.2.7 third-party/zlib @@ -769,11 +836,22 @@ make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/sort-bed/src' make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedmap/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects-typical/starchConstants.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedops/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers -mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] + 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] + 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../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:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; @@ -785,12 +863,17 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../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:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] + 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] + 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, @@ -833,6 +916,42 @@ from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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:359:87: note: length computed here + 359 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); + | ~~~~~~^~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/src/data/starch/starchHelpers.c:30: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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:383:48: note: length computed here + 383 | strncpy(*chr, s, strlen(s) + 1); + | ~~~~~~^~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/src/data/starch/starchHelpers.c:30: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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:485:77: note: length computed here + 485 | strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); + | ~~~~~~^~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/src/data/starch/starchHelpers.c:30: +In function 'char* strncpy(char*, const char*, size_t)', inlined from 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)' at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); @@ -841,7 +960,6 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: @@ -866,24 +984,46 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/src/data/starch/starchHelpers.c:30: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)' at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': +../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here + 560 | strncpy(*chr, 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:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] - 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../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:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] - 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] - 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../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:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] - 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)' at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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:311:47: note: length computed here + 311 | strncpy(iter->filename, fn, strlen(fn) + 1); + | ~~~~~~^~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)' at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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:330:59: note: length computed here + 330 | strncpy(iter->signature, signature, strlen(signature) + 1); + | ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ @@ -898,50 +1038,50 @@ from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: + inlined from 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:1411:97: note: length computed here - 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)': +../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here + 923 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); +In function 'char* strncat(char*, const char*, size_t)', + inlined from 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: 'char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:359:87: note: length computed here - 359 | strncpy(*chr, reinterpret_cast( buffer ), strlen(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:964:98: note: length computed here + 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32: + inlined from 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:383:48: note: length computed here - 383 | strncpy(*chr, s, strlen(s) + 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:1411:97: note: length computed here + 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16: + inlined from 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:485:77: note: length computed here - 485 | 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:1411:97: note: length computed here + 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: @@ -982,18 +1122,6 @@ from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)' at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': -../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~^~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/starchHelpers.c:30: -In function 'char* strncpy(char*, const char*, size_t)', inlined from 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)' at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); @@ -1016,27 +1144,63 @@ | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)' at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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:2228:57: note: length computed here + 2228 | strncpy(recTokBuf, token, strlen(token) + 1); + | ~~~~~~^~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)' at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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:2244:65: note: length computed here + 2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); + | ~~~~~~^~~~~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)' at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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:2256:59: note: length computed here + 2256 | strncpy(recFilename, token, strlen(token) + 1); + | ~~~~~~^~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28: + inlined from 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)' at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:923:97: note: length computed here - 923 | 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:2416:97: note: length computed here + 2416 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function 'char* strncat(char*, const char*, size_t)', - inlined from 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: + inlined from 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)' at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: 'char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:964:98: note: length computed here - 964 | 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:2464:98: note: length computed here + 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, @@ -1076,55 +1240,43 @@ | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/starchHelpers.c:30: + from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: + inlined from '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)' at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:1411:97: note: length computed here - 1411 | strncpy(prevChromosome, 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:1684:50: note: length computed here + 1684 | strncpy(*note, streamNote, strlen(streamNote) + 1); + | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/starchHelpers.c:30: + from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: + inlined from '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)' at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:1411:97: note: length computed here - 1411 | strncpy(prevChromosome, 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:1667:52: note: length computed here + 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); + | ~~~~~~^~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)' at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: + inlined from 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:2416:97: note: length computed here - 2416 | 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:1411:97: note: length computed here + 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: -In function 'char* strncat(char*, const char*, size_t)', - inlined from 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)' at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: 'char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:2464:98: note: length computed here - 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)' at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -1158,6 +1310,7 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: @@ -1170,91 +1323,79 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ -mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects-typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/starchHelpers.c:30: + from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)' at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28: + inlined from 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:3695:97: note: length computed here - 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_JSONMetadataExists(FILE**, const char*)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1096:20: warning: comparison is always true due to limited range of data type [-Wtype-limits] - 1096 | } while (currC != EOF); - | ^ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1097:63: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 1097 | if ((nReadBytes == STARCH_LEGACY_METADATA_SIZE) || (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:1313:24: warning: comparison is always true due to limited range of data type [-Wtype-limits] - 1313 | } while (currC != EOF); - | ^ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here + 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: + from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)' at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: + inlined from 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:311:47: note: length computed here - 311 | strncpy(iter->filename, fn, strlen(fn) + 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:1678:75: note: length computed here + 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: + from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)' at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: + inlined from 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:330:59: note: length computed here - 330 | strncpy(iter->signature, signature, strlen(signature) + 1); - | ~~~~~~^~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)' at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:2228:57: note: length computed here - 2228 | strncpy(recTokBuf, 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:1667:75: note: length computed here + 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: + from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)' at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32: + inlined from 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)' at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:2244:65: note: length computed here - 2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 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:3695:97: note: length computed here + 3695 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~^~~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: + from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)' at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + inlined from 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:2256:59: note: length computed here - 2256 | 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:200:32: note: length computed here + 200 | 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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects-typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_JSONMetadataExists(FILE**, const char*)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1096:20: warning: comparison is always true due to limited range of data type [-Wtype-limits] + 1096 | } while (currC != EOF); + | ^ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1097:63: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 1097 | if ((nReadBytes == STARCH_LEGACY_METADATA_SIZE) || (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:1313:24: warning: comparison is always true due to limited range of data type [-Wtype-limits] + 1313 | } while (currC != EOF); + | ^ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: @@ -1281,28 +1422,18 @@ | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from '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)' at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:1684:50: note: length computed here - 1684 | strncpy(*note, streamNote, strlen(streamNote) + 1); - | ~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: + from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function 'char* strncpy(char*, const char*, size_t)', - inlined from '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)' at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + inlined from 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:1667:52: note: length computed here - 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); - | ~~~~~~^~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: @@ -1339,7 +1470,7 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here 2256 | strncpy(recFilename, token, strlen(token) + 1); | ~~~~~~^~~~~~~ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: @@ -1364,7 +1495,7 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); | ~~~~~~^~~~~~~~~~~~~ -mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p ../bin && g++ -o ../bin/bedmap-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security 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 In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: @@ -1389,20 +1520,6 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'void starch::UNSTARCH_printMetadataSignature(const unsigned char*)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2276 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:2278:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2278 | 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:2640:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2640 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2642 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: @@ -1439,7 +1556,6 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: @@ -1476,6 +1592,7 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here 2256 | strncpy(recFilename, token, strlen(token) + 1); | ~~~~~~^~~~~~~ +mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: @@ -1500,55 +1617,20 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); | ~~~~~~^~~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here - 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here - 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here - 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:200:32: note: length computed here - 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.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:2276:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2276 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2278:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2278 | 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:2640:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2640 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2642 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: @@ -1597,18 +1679,19 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: + inlined from 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:2559:40: note: length computed here - 2559 | 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:200:32: note: length computed here + 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: @@ -1621,20 +1704,9 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:200:32: note: length computed here - 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers +mkdir -p ../bin && g++ -o ../bin/bedops-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security 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/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: @@ -1647,13 +1719,10 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -mkdir -p ../bin && g++ -o ../bin/bedmap-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security 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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -mkdir -p ../bin && g++ -o ../bin/bedops-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedops.cpp +mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers +mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from SortDetails.cpp:30: @@ -1666,20 +1735,6 @@ SortDetails.cpp:249:25: note: length computed here 249 | chromBufLen = strlen(chromBuf); // we know >= 1 | ~~~~~~^~~~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from SortDetails.cpp:30: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void lexSortBedData(BedData*)' at SortDetails.cpp:1343:20: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SortDetails.cpp: In function 'void lexSortBedData(BedData*)': -SortDetails.cpp:1342:33: note: length computed here - 1342 | chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1 - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers -mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security 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*)': @@ -1716,6 +1771,26 @@ | ^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, + from SortDetails.cpp:30: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void lexSortBedData(BedData*)' at SortDetails.cpp:1343:20: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SortDetails.cpp: In function 'void lexSortBedData(BedData*)': +SortDetails.cpp:1342:33: note: length computed here + 1342 | chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1 + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/closestfeats/src -f Makefile build +make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/closestfeats/src' +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, @@ -1765,6 +1840,21 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here 556 | std::strncpy(_recFilename, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] + 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] + 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../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:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] + 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] + 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, @@ -1994,241 +2084,6 @@ | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from Bedops.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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*)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here - 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); - | ~~~~~~^~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from Bedops.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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*)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here - 551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); - | ~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from Bedops.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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*)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here - 556 | std::strncpy(_recFilename, _token, strlen(_token) + 1); - | ~~~~~~^~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from Bedops.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 member function 'const char* starch::Starch::getCurrentChromosome()': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from Bedops.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::Starch::zReadLine()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 member function 'int starch::Starch::zReadLine()': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here - 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from Bedops.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, - inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1769:45: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 member function 'int starch::Starch::extractLine(std::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from Bedops.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, - inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 member function 'int starch::Starch::extractLine(std::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from Bedops.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentRemainder(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24, - inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 member function 'int starch::Starch::extractLine(std::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here - 899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); - | ~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from Bedops.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - 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::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 member function 'bool starch::Starch::extractBEDLine(std::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from Bedops.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, - inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 member function 'bool starch::Starch::extractBEDLine(std::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from Bedops.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - 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::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 member function 'bool starch::Starch::extractBEDLine(std::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, - from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, - from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, - from CheckSort.cpp:28: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - 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; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, - from CheckSort.cpp:28: -../../../../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; unsigned int SZ = 16]': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, - from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, - from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, - from CheckSort.cpp:28: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - 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::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36, - inlined from 'int checkSort(const char**, unsigned int)' at CheckSort.cpp:51:28: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, - from CheckSort.cpp:28: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function 'int checkSort(const char**, unsigned int)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -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 -mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -s -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -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-2.4.39+dfsg1/applications/bed/sort-bed/src' -make -C applications/bed/closestfeats/src -f Makefile build -make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/closestfeats/src' -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': -../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] - 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] - 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../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:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] - 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] - 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)' at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32: @@ -2432,6 +2287,26 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here 1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); | ~~~~~~^~~~~~~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, + from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, + from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, + from CheckSort.cpp:28: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + 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; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, + from CheckSort.cpp:28: +../../../../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; unsigned int SZ = 16]': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, @@ -2471,138 +2346,111 @@ | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: + from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27, + from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, + from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, + from CheckSort.cpp:28: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + 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::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36, + inlined from 'int checkSort(const char**, unsigned int)' at CheckSort.cpp:51:28: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:200:32: note: length computed here - 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, + from CheckSort.cpp:28: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function 'int checkSort(const char**, unsigned int)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: + inlined from 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:2559:40: note: length computed here - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -mkdir -p ../bin && g++ -o ../bin/closest-features-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security 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/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here + 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: + from Bedops.cpp:26: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: + from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: + from Bedops.cpp:26: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: + from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here 551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); | ~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: + from Bedops.cpp:26: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: + from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here 556 | std::strncpy(_recFilename, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::Starch::zReadLine()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here - 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, - inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1521:82: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: + from Bedops.cpp:26: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, - inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1712:86: + inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': + from Bedops.cpp:41: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'const char* starch::Starch::getCurrentChromosome()': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: + from Bedops.cpp:26: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, - inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1758:40: + inlined from 'int starch::Starch::zReadLine()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ + from Bedops.cpp:41: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here + 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: + from Bedops.cpp:26: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, @@ -2611,46 +2459,14 @@ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, - inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1576:86: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, - inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1620:40: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: + from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: + from Bedops.cpp:26: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, @@ -2659,14 +2475,14 @@ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: + from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: + from Bedops.cpp:26: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'void starch::Starch::setCurrentRemainder(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24, inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36: @@ -2674,78 +2490,23 @@ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: + from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here 899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - 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::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, - inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - 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::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from Bedops.cpp:26: + from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - 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::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + inlined from 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 function 'Bed::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 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:2559:40: note: length computed here + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from Bedops.cpp:26: @@ -2753,30 +2514,13 @@ inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, 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::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36: + inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 function 'Bed::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - 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; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; unsigned int SZ = 512]': +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ @@ -2785,69 +2529,14 @@ from Bedops.cpp:26: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - 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::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36, - inlined from 'BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]' at BedPadReader.hpp:140:11: + inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, + inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 member function 'BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - 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::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36, - inlined from 'FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]' at BedReader.hpp:78:19: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - 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::allocate_iterator_starch_bed::allocate_iterator_starch_bed(Ext::FPWrap&, Ext::PooledMemory&, const string&) [with ErrorType = Ext::Exception, 0>; BedType = Bed::BasicCoords; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:117:36: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor 'Bed::allocate_iterator_starch_bed::allocate_iterator_starch_bed(Ext::FPWrap&, Ext::PooledMemory&, const string&) [with ErrorType = Ext::Exception, 0>; BedType = Bed::BasicCoords; unsigned int SZ = 512]': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ClosestFeature.cpp:26: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - 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::allocate_iterator_starch_bed Bed::allocate_iterator_starch_bed::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:207:36, - inlined from 'FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]' at BedReader.hpp:78:19: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, - from ClosestFeature.cpp:38: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]': +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ @@ -2858,22 +2547,25 @@ inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, 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::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36, - inlined from 'BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]' at BedPadReader.hpp:140:11: + inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 member function 'BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]': +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ -rm -rf objects_typical -make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/closestfeats/src' +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers +mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -s -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -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-2.4.39+dfsg1/applications/bed/sort-bed/src' make -C applications/bed/bedextract/src -f Makefile build make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedextract/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers +mkdir -p ../bin && g++ -o ../bin/closest-features-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security 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_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers @@ -3099,6 +2791,48 @@ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, + from ClosestFeature.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here + 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); + | ~~~~~~^~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ClosestFeature.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here + 551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); + | ~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ClosestFeature.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here + 556 | std::strncpy(_recFilename, _token, strlen(_token) + 1); + | ~~~~~~^~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: @@ -3135,89 +2869,195 @@ | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: + from ClosestFeature.cpp:26: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + inlined from 'int starch::Starch::zReadLine()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:200:32: note: length computed here - 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here + 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: + from ClosestFeature.cpp:26: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, + inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1521:82: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:2559:40: note: length computed here - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -mkdir -p ../bin && g++ -o ../bin/bedextract-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security 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 -rm -rf objects_typical -make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedops/src' -make -C applications/bed/starch/src -f Makefile build -make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/starch/src' -mkdir -p objects -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchConstants.c -o objects/starchConstants.o -iquote../../../../interfaces/general-headers -iquote../../../.. -mkdir -p objects -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects/unstarchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'void starch::UNSTARCH_printMetadataSignature(const unsigned char*)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2276 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:2278:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2278 | 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:2640:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2640 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2642 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: + from ClosestFeature.cpp:26: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, + inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1712:86: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here - 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: + from ClosestFeature.cpp:26: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, + inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1758:40: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here - 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: + from ClosestFeature.cpp:26: In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, + inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1769:45: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here - 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ClosestFeature.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, + inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1576:86: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ClosestFeature.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, + inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1620:40: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ClosestFeature.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, + inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ClosestFeature.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentRemainder(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24, + inlined from 'int starch::Starch::extractLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here + 899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); + | ~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ClosestFeature.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + 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::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ClosestFeature.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37, + inlined from 'bool starch::Starch::extractBEDLine(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ClosestFeature.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + 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::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::string&)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: @@ -3232,6 +3072,21 @@ | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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:2559:40: note: length computed here + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers +mkdir -p ../bin && g++ -o ../bin/bedextract-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security 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 +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: @@ -3415,18 +3270,6 @@ | ~~~~~~^~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:2559:40: note: length computed here - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, from ExtractRows.cpp:27: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, @@ -3475,6 +3318,148 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ +In file included from /usr/include/c++/10/map:60, + from ExtractRows.cpp:33: +/usr/include/c++/10/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = Bed::BasicCoords; _Val = std::pair, long long int>; _KeyOfValue = std::_Select1st, long long int> >; _Compare = Bed::extract_details::CompBed >; _Alloc = std::allocator, long long int> >]': +/usr/include/c++/10/bits/stl_tree.h:2524:5: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, Bed::extract_details::CompBed >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 + 2524 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_tree.h:2524:5: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, Bed::extract_details::CompBed >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_tree.h: In function 'std::pair Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = __gnu_cxx::__normal_iterator**, std::vector*> >; Op = {anonymous}::Cache >]': +/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, Bed::extract_details::CompBed >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 + 1245 | _M_erase_aux(__first, __last); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_tree.h: In function 'std::pair Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = __gnu_cxx::__normal_iterator**, std::vector*> >; Op = Visitors::BedHelpers::Println]': +/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, Bed::extract_details::CompBed >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 + 1245 | _M_erase_aux(__first, __last); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ExtractRows.cpp:27: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + 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; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, + from ExtractRows.cpp:43: +../../../../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; unsigned int SZ = 16]': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ +In file included from /usr/include/c++/10/map:60, + from ExtractRows.cpp:33: +/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, Bed::extract_details::CompBed >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 + 1245 | _M_erase_aux(__first, __last); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ExtractRows.cpp:27: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + 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::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36, + inlined from 'std::pair Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = Bed::bed_check_iterator*, 16>; Op = Visitors::BedHelpers::Println]' at ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:102:64: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, + from ExtractRows.cpp:43: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function 'std::pair Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = Bed::bed_check_iterator*, 16>; Op = Visitors::BedHelpers::Println]': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ +In file included from /usr/include/c++/10/map:60, + from ExtractRows.cpp:33: +/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, Bed::extract_details::CompBed >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 + 1245 | _M_erase_aux(__first, __last); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +rm -rf objects_typical +make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedextract/src' +make -C applications/bed/starch/src -f Makefile build +make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/applications/bed/starch/src' +mkdir -p objects +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchConstants.c -o objects/starchConstants.o -iquote../../../../interfaces/general-headers -iquote../../../.. +mkdir -p objects +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects/unstarchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'void starch::UNSTARCH_printMetadataSignature(const unsigned char*)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2276 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2278:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2278 | 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:2640:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2640 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2642 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here + 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here + 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here + 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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:200:32: note: length computed here + 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)' at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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:2559:40: note: length computed here + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -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::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': @@ -3575,13 +3560,6 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here 1411 | strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/map:60, - from ExtractRows.cpp:33: -/usr/include/c++/10/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = Bed::BasicCoords; _Val = std::pair, long long int>; _KeyOfValue = std::_Select1st, long long int> >; _Compare = Bed::extract_details::CompBed >; _Alloc = std::allocator, long long int> >]': -/usr/include/c++/10/bits/stl_tree.h:2524:5: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, Bed::extract_details::CompBed >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 - 2524 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_tree.h:2524:5: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, Bed::extract_details::CompBed >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: @@ -3606,14 +3584,6 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_tree.h: In function 'std::pair Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = __gnu_cxx::__normal_iterator**, std::vector*> >; Op = {anonymous}::Cache >]': -/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, Bed::extract_details::CompBed >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 - 1245 | _M_erase_aux(__first, __last); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_tree.h: In function 'std::pair Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = __gnu_cxx::__normal_iterator**, std::vector*> >; Op = Visitors::BedHelpers::Println]': -/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, Bed::extract_details::CompBed >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 - 1245 | _M_erase_aux(__first, __last); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchHelpers.c:30: @@ -3701,28 +3671,6 @@ | ~~~~~~^~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, - from ExtractRows.cpp:27: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - 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; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, - from ExtractRows.cpp:43: -../../../../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; unsigned int SZ = 16]': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -In file included from /usr/include/c++/10/map:60, - from ExtractRows.cpp:33: -/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, Bed::extract_details::CompBed >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 - 1245 | _M_erase_aux(__first, __last); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30: In function 'char* strncpy(char*, const char*, size_t)', inlined from '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)' at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24: @@ -3747,31 +3695,8 @@ | ~~~~~~^~~~~~~~~~~~~ mkdir -p objects g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects/starchFileHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. -In file included from /usr/include/string.h:495, - from /usr/include/c++/10/cstring:42, - from ExtractRows.cpp:27: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, - 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::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36, - inlined from 'std::pair Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = Bed::bed_check_iterator*, 16>; Op = Visitors::BedHelpers::Println]' at ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:102:64: -/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, - from ExtractRows.cpp:43: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function 'std::pair Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = Bed::bed_check_iterator*, 16>; Op = Visitors::BedHelpers::Println]': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ mkdir -p objects g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../.. -In file included from /usr/include/c++/10/map:60, - from ExtractRows.cpp:33: -/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long int>, std::_Select1st, long long int> >, Bed::extract_details::CompBed >, std::allocator, long long int> > >::const_iterator' changed in GCC 7.1 - 1245 | _M_erase_aux(__first, __last); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ mkdir -p objects g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects/starchBase64Coding.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p ../bin @@ -3867,6 +3792,23 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security objects/unstarch.o -o ../bin/unstarch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now mkdir -p ../bin g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c starchcat.c -o objects/starchcat.o -iquote../../../../interfaces/general-headers -iquote../../../.. +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ClosestFeature.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + 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; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; unsigned int SZ = 512]': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ In file included from /usr/include/c++/10/cassert:44, from starchcat.c:33: starchcat.c: In function 'int main(int, char**)': @@ -4012,30 +3954,59 @@ starchcat.c:7060:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 7060 | UNSTARCH_reverseTransformCoordinates( static_cast( *t_lineIdxPtr ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -rm -rf objects_typical -make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedextract/src' -make -C applications/bed/conversion/src -f Makefile build -make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/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 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -iquote"/build/bedops-2.4.39+dfsg1/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" -Wl,-z,relro -Wl,-z,now convert2bed.c -o ../bin/convert2bed-typical -lpthread -convert2bed.c: In function 'c2b_process_intermediate_bytes_by_lines': -convert2bed.c:6315:103: warning: format '%zu' expects argument of type 'size_t', but argument 3 has type 'long unsigned int' [-Wformat=] - 6315 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity); - | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | unsigned int long unsigned int - | %lu -convert2bed.c:6315:109: warning: format '%zu' expects argument of type 'size_t', but argument 4 has type 'long unsigned int' [-Wformat=] - 6315 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity); - | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | unsigned int long unsigned int - | %lu -convert2bed.c:6315:115: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'long unsigned int' [-Wformat=] - 6315 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity); - | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | unsigned int long unsigned int - | %lu +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ClosestFeature.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + 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::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36, + inlined from 'FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]' at BedReader.hpp:78:19: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ClosestFeature.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + 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::allocate_iterator_starch_bed::allocate_iterator_starch_bed(Ext::FPWrap&, Ext::PooledMemory&, const string&) [with ErrorType = Ext::Exception, 0>; BedType = Bed::BasicCoords; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:117:36: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor 'Bed::allocate_iterator_starch_bed::allocate_iterator_starch_bed(Ext::FPWrap&, Ext::PooledMemory&, const string&) [with ErrorType = Ext::Exception, 0>; BedType = Bed::BasicCoords; unsigned int SZ = 512]': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from ClosestFeature.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + 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::allocate_iterator_starch_bed Bed::allocate_iterator_starch_bed::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:207:36, + inlined from 'FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]' at BedReader.hpp:78:19: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, + from ClosestFeature.cpp:38: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from starchcat.c:31: @@ -4060,6 +4031,23 @@ starchcat.c:3123:78: note: length computed here 3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); | ~~~~~~^~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from Bedops.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + 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::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 function 'Bed::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security objects/starchcat.o -o ../bin/starchcat-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now mkdir -p ../bin g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -c starchstrip.c -o objects/starchstrip.o -iquote../../../../interfaces/general-headers -iquote../../../.. @@ -4071,10 +4059,89 @@ 126 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security objects/starchstrip.o -o ../bin/starchstrip-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from Bedops.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + 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::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 function 'Bed::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ rm -rf objects make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/starch/src' +make -C applications/bed/conversion/src -f Makefile build +make[4]: Entering directory '/build/bedops-2.4.39+dfsg1/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 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -O2 -fdebug-prefix-map=/build/bedops-2.4.39+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -iquote"/build/bedops-2.4.39+dfsg1/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" -Wl,-z,relro -Wl,-z,now convert2bed.c -o ../bin/convert2bed-typical -lpthread +convert2bed.c: In function 'c2b_process_intermediate_bytes_by_lines': +convert2bed.c:6315:103: warning: format '%zu' expects argument of type 'size_t', but argument 3 has type 'long unsigned int' [-Wformat=] + 6315 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity); + | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | unsigned int long unsigned int + | %lu +convert2bed.c:6315:109: warning: format '%zu' expects argument of type 'size_t', but argument 4 has type 'long unsigned int' [-Wformat=] + 6315 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity); + | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | unsigned int long unsigned int + | %lu +convert2bed.c:6315:115: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'long unsigned int' [-Wformat=] + 6315 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity); + | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | unsigned int long unsigned int + | %lu +rm -rf objects_typical +make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/closestfeats/src' +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from Bedops.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + 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::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36, + inlined from 'BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]' at BedPadReader.hpp:140:11: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 member function 'BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ rm -rf objects make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/conversion/src' +In file included from /usr/include/string.h:495, + from /usr/include/c++/10/cstring:42, + from Bedops.cpp:26: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'void starch::Starch::setCurrentChromosome(char*)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24, + 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::allocate_iterator_starch_bed& Bed::allocate_iterator_starch_bed::operator++() [with BedType = Bed::BasicCoords; unsigned int SZ = 512]' at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36, + inlined from 'BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]' at BedPadReader.hpp:140:11: +/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 member function 'BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed*, 512>]': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ +rm -rf objects_typical +make[4]: Leaving directory '/build/bedops-2.4.39+dfsg1/applications/bed/bedops/src' In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:28, @@ -4609,7 +4676,7 @@ dh_testroot dh_prep dh_auto_install - make -j3 install DESTDIR=/build/bedops-2.4.39\+dfsg1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + make -j4 install DESTDIR=/build/bedops-2.4.39\+dfsg1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bedops-2.4.39+dfsg1' mkdir -p bin cp applications/bed/conversion/src/wrappers/bam2bed applications/bed/conversion/src/wrappers/bam2bed_gnuParallel applications/bed/conversion/src/wrappers/bam2bed_sge applications/bed/conversion/src/wrappers/bam2bed_slurm applications/bed/conversion/src/wrappers/bam2starch applications/bed/conversion/src/wrappers/bam2starch_gnuParallel applications/bed/conversion/src/wrappers/bam2starch_sge applications/bed/conversion/src/wrappers/bam2starch_slurm applications/bed/conversion/src/wrappers/gff2bed applications/bed/conversion/src/wrappers/gff2starch applications/bed/conversion/src/wrappers/gtf2bed applications/bed/conversion/src/wrappers/gtf2starch applications/bed/conversion/src/wrappers/gvf2bed applications/bed/conversion/src/wrappers/gvf2starch applications/bed/conversion/src/wrappers/psl2bed applications/bed/conversion/src/wrappers/psl2starch applications/bed/conversion/src/wrappers/rmsk2bed applications/bed/conversion/src/wrappers/rmsk2starch applications/bed/conversion/src/wrappers/sam2bed applications/bed/conversion/src/wrappers/sam2starch applications/bed/conversion/src/wrappers/vcf2bed applications/bed/conversion/src/wrappers/vcf2starch applications/bed/conversion/src/wrappers/wig2bed applications/bed/conversion/src/wrappers/wig2starch bin @@ -4650,7 +4717,7 @@ app.add_stylesheet("custom.css") loading intersphinx inventory from http://docs.python.org/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'http://docs.python.org/objects.inv' not fetchable due to : HTTPConnectionPool(host='docs.python.org', port=80): Max retries exceeded with url: /objects.inv (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')) +intersphinx inventory 'http://docs.python.org/objects.inv' not fetchable due to : HTTPConnectionPool(host='docs.python.org', port=80): Max retries exceeded with url: /objects.inv (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')) building [mo]: targets for 0 po files that are out of date building [html]: targets for 47 source files that are out of date updating environment: [new config] 47 added, 0 changed, 0 removed @@ -4881,235 +4948,235 @@ dh_perl dh_link dh_strip_nondeterminism -debian/bedops-doc/usr/share/doc/bedops/html/_static/bedops_macosx_installer_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_bedextract_nested_elements.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/bedops_macosx_installer_screen_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/BEDOPS_Presentation_starch_efficiency.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/BEDOPS_Presentation_bedmap_ops.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_elementof_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_elementof_ba.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/bedops_cygwin_installer_git_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_everything.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_symmetricdifference_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/statistics.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_difference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/starch_specification_padding.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_merge_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/starch_specification_metadata.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/set_operations_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_everything@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/other.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/macosx_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/support_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_bedops_intersect_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/SNP_DHS_matrix_diseaseSorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/file_management_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_inputs@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_intersect_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_complement_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/reference_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_partition_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_stagger_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/starchcluster_mechanism.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/macosx_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_merge_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/bedops_cygwin_installer_git_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/macosx.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_bedmap_mapref_all.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_partition_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/performance.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_bedops_merge_unsorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_complement_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/quick_start.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_chop_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/toc_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/set_operations.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_elementof_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/starch_specification_magicbytes.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/bioinformatics.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/starch_specification.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/source.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/documentation.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/downloads_v3.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_merge_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_inputs@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_bedmap_mapref_ref1.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/macosx_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_partition_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_inputs.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/statistics_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_complement_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/BEDOPS_Presentation_starch_efficiency.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_inputs.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_bedextract_mechanism.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_unstarch_extractiontime.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_notelementof_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/starch_specification_metadataoffset.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_notelementof_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_chop_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/SNP_DHS_matrix.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_elementof_ba@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/set_operations_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/BEDOPS_Presentation_bedmap_ops.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_chop_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_bedextract_nested_elements.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/toc_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_intersect_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/note.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -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 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_everything@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_bedmap_mapref_ref3.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_elementof_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/index/set_operations_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_bedops_complement_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/index/performance.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_inputs@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/performance.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_symmetricdifference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/index/linux.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_partition_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/index/support.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_chop_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -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 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/linux.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/index/file_management_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/support_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_bedmap_mapref_ref2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/index/source.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -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 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_complement_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -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 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/index/support_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/support.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -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 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/index/downloads_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_difference_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -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 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/index/macosx.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -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 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/starch_specification_metadatachecksum.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/index/other.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -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 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/bedops_macosx_installer_icon.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/index/downloads_v3.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/set_operations_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/index/source_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. 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/usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_stagger_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_difference_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/downloads_v3.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_images/source_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/usage-examples/SNP_DHS_matrix_diseaseSorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_elementof_ba@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_notelementof_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/BEDOPS_Presentation_grok_tests.png: 1 bytes of garbage 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/usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_stagger_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/support.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_merge_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_starch_efficiency.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/statistics_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_bedops_merge_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_everything.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/note.png: 1 bytes of garbage after IEND chunk at 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line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_merge_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/source_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/installation/bedops_macosx_installer_icon.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/starch_specification_chromosomestreams.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/installation/bedops_macosx_installer_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_bedextract_mechanism.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_difference_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/installation/bedops_cygwin_installer_git_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_cygwin_installer_gcc_screen.png: 1 bytes of garbage after IEND chunk at 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/usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. 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 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/statistics_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_bedops_merge_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/overview/BEDOPS_Presentation_starch_efficiency.png: 1 bytes of garbage after IEND chunk at 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172. -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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/bedops_macosx_installer_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/statistics/reference_bedmap_mapref_ref3.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/linux_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. 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/usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/file-management/compression/starch_specification.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/file-management/compression/starch_specification_metadatachecksum.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_starch_efficiency.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/file-management/compression/starch_specification_magicbytes.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/overview.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/file-management/compression/starch_specification_chromosomestreams.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/file-management/compression/starch_specification_metadata.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/file_management.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/file-management/compression/starch_specification_padding.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_symmetricdifference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/file-management/compression/starch_specification_metadataoffset.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/quick_start.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/starch_specification_metadata.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_elementof_ba.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_everything.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_difference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_intersect_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_complement_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_chop_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_chop_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_complement_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_difference_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_bedextract_mechanism.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_inputs.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_elementof_ba.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/statistics_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/readme/documentation.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/statistics.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_symmetricdifference_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/readme/overview.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/downloads_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_complement_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/readme/bioinformatics.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/file_management.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_independent_grok.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/usage-examples/SNP_DHS_matrix_diseaseSorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/source_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_bedmap_inputs.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/usage-examples/SNP_DHS_matrix.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/quick_start.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/performance_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/linux.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/set_operations_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. +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 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/linux_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +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 172. dh_compress dh_fixperms dh_missing @@ -5122,18 +5189,18 @@ dh_strip dh_makeshlibs dh_shlibdeps -dpkg-shlibdeps: warning: debian/bedops/usr/bin/bedmap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/bedops/usr/bin/closest-features contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bedops/usr/bin/sort-bed contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bedops/usr/bin/bedextract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bedops/usr/bin/closest-features contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bedops/usr/bin/bedmap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bedops/usr/bin/bedops contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/bedops/usr/bin/sort-bed contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'bedops-doc' in '../bedops-doc_2.4.39+dfsg1-2_all.deb'. dpkg-deb: building package 'bedops' in '../bedops_2.4.39+dfsg1-2_armhf.deb'. dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.39+dfsg1-2_armhf.deb'. +dpkg-deb: building package 'bedops-doc' in '../bedops-doc_2.4.39+dfsg1-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bedops_2.4.39+dfsg1-2_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -5141,12 +5208,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/30359/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30359/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/28355 and its subdirectories -I: Current time: Wed Jul 28 05:21:31 -12 2021 -I: pbuilder-time-stamp: 1627492891 +I: removing directory /srv/workspace/pbuilder/30359 and its subdirectories +I: Current time: Thu Jul 29 07:47:54 +14 2021 +I: pbuilder-time-stamp: 1627494474