Diff of the two buildlogs: -- --- b1/build.log 2023-01-05 18:52:15.570199210 +0000 +++ b2/build.log 2023-01-05 18:56:42.397180383 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 5 06:50:02 -12 2023 -I: pbuilder-time-stamp: 1672944602 +I: Current time: Thu Feb 8 15:15:19 +14 2024 +I: pbuilder-time-stamp: 1707354919 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./bedtools_2.30.0+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig._cfh5Q7H/trustedkeys.kbx': General error -gpgv: Signature made Wed Jan 27 04:27:58 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.CQlzbRav/trustedkeys.kbx': General error +gpgv: Signature made Thu Jan 28 06:27:58 2021 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bedtools_2.30.0+dfsg-1.dsc @@ -33,135 +33,170 @@ dpkg-source: info: applying htsutil I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3368056/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1785102/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +lrwxrwxrwx 1 root root 4 Feb 8 15:15 /bin/sh -> 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/1785102/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1785102/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + 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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='096f5d5dc4ec404ba8cca7b30adba40d' - 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='3368056' - PS1='# ' - PS2='> ' + INVOCATION_ID=f4213f25deea429eb497ee407443d00c + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1785102 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/r-b-build.HdfcE4I0/pbuilderrc_IuB5 --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HdfcE4I0/b1 --logfile b1/build.log bedtools_2.30.0+dfsg-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.HdfcE4I0/pbuilderrc_n8Kc --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HdfcE4I0/b2 --logfile b2/build.log bedtools_2.30.0+dfsg-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.0.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.0.12-1~bpo11+1 (2022-12-19) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 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 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 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 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jan 20 2022 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 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jan 20 2022 more - -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount - -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Dec 20 21:25 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jan 20 2022 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/3368056/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 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 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 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 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jan 21 2022 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 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jan 21 2022 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jan 21 2022 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jan 21 2022 more + -rwsr-xr-x 1 root root 55528 Jan 21 2022 mount + -rwxr-xr-x 1 root root 18664 Jan 21 2022 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Feb 8 15:15 sh -> bash + lrwxrwxrwx 1 root root 4 Jan 24 05:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jan 21 2022 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jan 21 2022 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jan 21 2022 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/1785102/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -251,7 +286,7 @@ Get: 44 http://deb.debian.org/debian bullseye/main amd64 libbz2-dev amd64 1.0.8-4 [30.1 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 liblzma-dev amd64 5.2.5-2.1~deb11u1 [229 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] -Fetched 24.2 MB in 1s (24.7 MB/s) +Fetched 24.2 MB in 8s (2960 kB/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 ... 19704 files and directories currently installed.) @@ -453,7 +488,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/bedtools-2.30.0+dfsg/ && 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 > ../bedtools_2.30.0+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/1785102/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/1785102/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/bedtools-2.30.0+dfsg/ && 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 > ../bedtools_2.30.0+dfsg-1_source.changes dpkg-buildpackage: info: source package bedtools dpkg-buildpackage: info: source version 2.30.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -465,7 +504,7 @@ dh clean dh_auto_clean install -d /build/bedtools-2.30.0\+dfsg/debian/.debhelper/generated/_source/home - make -j15 clean + make -j16 clean make[1]: Entering directory '/build/bedtools-2.30.0+dfsg' * Cleaning up. make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. @@ -492,7 +531,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/bedtools-2.30.0+dfsg' dh_auto_build -- VERBOSE=1 - make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 + make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/bedtools-2.30.0+dfsg' Building BEDTools: cd src/utils/htslib && make config.h @@ -503,82 +542,82 @@ make[3]: Entering directory '/build/bedtools-2.30.0+dfsg/src/utils/htslib' CXXFLAGS is [-g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security] * compiling src/bedtools.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedtools.o -MMD -MP -MF obj/bedtools.Td -c -o obj/bedtools.o src/bedtools.cpp * compiling src/htsutil.cpp * compiling src/annotateBed/annotateMain.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/htsutil.o -MMD -MP -MF obj/htsutil.Td -c -o obj/htsutil.o src/htsutil.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedtools.o -MMD -MP -MF obj/bedtools.Td -c -o obj/bedtools.o src/bedtools.cpp * compiling src/annotateBed/annotateBed.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/htsutil.o -MMD -MP -MF obj/htsutil.Td -c -o obj/htsutil.o src/htsutil.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/annotateMain.o -MMD -MP -MF obj/annotateMain.Td -c -o obj/annotateMain.o src/annotateBed/annotateMain.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/annotateBed.o -MMD -MP -MF obj/annotateBed.Td -c -o obj/annotateBed.o src/annotateBed/annotateBed.cpp * compiling src/bamToBed/bamToBed.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bamToBed.o -MMD -MP -MF obj/bamToBed.Td -c -o obj/bamToBed.o src/bamToBed/bamToBed.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/annotateBed.o -MMD -MP -MF obj/annotateBed.Td -c -o obj/annotateBed.o src/annotateBed/annotateBed.cpp * compiling src/bamToFastq/bamToFastqMain.cpp - * compiling src/bamToFastq/bamToFastq.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bamToBed.o -MMD -MP -MF obj/bamToBed.Td -c -o obj/bamToBed.o src/bamToBed/bamToBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bamToFastqMain.o -MMD -MP -MF obj/bamToFastqMain.Td -c -o obj/bamToFastqMain.o src/bamToFastq/bamToFastqMain.cpp + * compiling src/bamToFastq/bamToFastq.cpp * compiling src/bedToBam/bedToBam.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bamToFastq.o -MMD -MP -MF obj/bamToFastq.Td -c -o obj/bamToFastq.o src/bamToFastq/bamToFastq.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders 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-DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bamToFastq.o -MMD -MP -MF obj/bamToFastq.Td -c -o obj/bamToFastq.o src/bamToFastq/bamToFastq.cpp * compiling src/bedToIgv/bedToIgv.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 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-Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedpeToBam.o -MMD -MP -MF obj/bedpeToBam.Td -c -o obj/bedpeToBam.o src/bedpeToBam/bedpeToBam.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap 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-Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedpeToBam.o -MMD -MP -MF obj/bedpeToBam.Td -c -o obj/bedpeToBam.o src/bedpeToBam/bedpeToBam.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedToIgv.o -MMD -MP -MF obj/bedToIgv.Td -c -o obj/bedToIgv.o src/bedToIgv/bedToIgv.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bed12ToBed6.o -MMD -MP -MF obj/bed12ToBed6.Td -c -o obj/bed12ToBed6.o src/bed12ToBed6/bed12ToBed6.cpp * compiling src/closestFile/closestHelp.cpp - * compiling src/closestFile/closestFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/closestHelp.o -MMD -MP -MF obj/closestHelp.Td -c -o obj/closestHelp.o src/closestFile/closestHelp.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/closestFile.o -MMD -MP -MF obj/closestFile.Td -c -o obj/closestFile.o src/closestFile/closestFile.cpp echo '/* Default config.h generated by Makefile */' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h + * compiling src/closestFile/closestFile.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/closestFile.o -MMD -MP -MF obj/closestFile.Td -c -o obj/closestFile.o src/closestFile/closestFile.cpp + * compiling src/clusterBed/clusterMain.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/clusterMain.o -MMD -MP -MF obj/clusterMain.Td -c -o obj/clusterMain.o src/clusterBed/clusterMain.cpp echo '#ifndef __APPLE__' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#endif' >> config.h echo '#define HAVE_FSEEKO 1' >> config.h -echo '#define HAVE_DRAND48 1' >> config.h - * compiling src/clusterBed/clusterMain.cpp -make[3]: Leaving directory '/build/bedtools-2.30.0+dfsg/src/utils/htslib' -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/clusterMain.o -MMD -MP -MF obj/clusterMain.Td -c -o obj/clusterMain.o src/clusterBed/clusterMain.cpp * compiling src/clusterBed/clusterBed.cpp +echo '#define HAVE_DRAND48 1' >> config.h g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/clusterBed.o -MMD -MP -MF obj/clusterBed.Td -c -o obj/clusterBed.o src/clusterBed/clusterBed.cpp -In file included from src/utils/BamTools/include/api/BamReader.h:1, - from src/bamToFastq/bamToFastq.h:15, - from src/bamToFastq/bamToFastq.cpp:15: -src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': -src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 32 | sam_hdr_write(fp, hdr); - | ~~~~~~~~~~~~~^~~~~~~~~ -src/clusterBed/clusterMain.cpp: In function 'int cluster_main(int, char**)': -src/clusterBed/clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable] - 38 | bool haveMaxDistance = false; - | ^~~~~~~~~~~~~~~ -src/bedToBam/bedToBam.cpp: In function 'int bedtobam_main(int, char**)': -src/bedToBam/bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable] - 60 | bool haveMapQual = false; - | ^~~~~~~~~~~ +make[3]: Leaving directory '/build/bedtools-2.30.0+dfsg/src/utils/htslib' + * compiling src/complementFile/complementHelp.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/complementHelp.o -MMD -MP -MF obj/complementHelp.Td -c -o obj/complementHelp.o src/complementFile/complementHelp.cpp src/bamToFastq/bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)': src/bamToFastq/bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable] 38 | bool haveFastq2 = false; | ^~~~~~~~~~ +src/clusterBed/clusterMain.cpp: In function 'int cluster_main(int, char**)': +src/clusterBed/clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable] + 38 | bool haveMaxDistance = false; + | ^~~~~~~~~~~~~~~ + * compiling src/complementFile/complementFile.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/complementFile.o -MMD -MP -MF obj/complementFile.Td -c -o obj/complementFile.o src/complementFile/complementFile.cpp src/bedpeToBam/bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)': src/bedpeToBam/bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable] 61 | bool haveMapQual = false; | ^~~~~~~~~~~ - * compiling src/complementFile/complementHelp.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/complementHelp.o -MMD -MP -MF obj/complementHelp.Td -c -o obj/complementHelp.o src/complementFile/complementHelp.cpp - * compiling src/complementFile/complementFile.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/complementFile.o -MMD -MP -MF obj/complementFile.Td -c -o obj/complementFile.o src/complementFile/complementFile.cpp * compiling src/coverageFile/coverageHelp.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/coverageHelp.o -MMD -MP -MF obj/coverageHelp.Td -c -o obj/coverageHelp.o src/coverageFile/coverageHelp.cpp +src/bedToBam/bedToBam.cpp: In function 'int bedtobam_main(int, char**)': +src/bedToBam/bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable] + 60 | bool haveMapQual = false; + | ^~~~~~~~~~~ + * compiling src/coverageFile/coverageFile.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/coverageFile.o -MMD -MP -MF obj/coverageFile.Td -c -o obj/coverageFile.o src/coverageFile/coverageFile.cpp src/bamToBed/bamToBed.cpp: In function 'int bamtobed_main(int, char**)': src/bamToBed/bamToBed.cpp:88:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable] 88 | bool useAlignmentScore = false; | ^~~~~~~~~~~~~~~~~ - * compiling src/coverageFile/coverageFile.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/coverageFile.o -MMD -MP -MF obj/coverageFile.Td -c -o obj/coverageFile.o src/coverageFile/coverageFile.cpp * compiling src/expand/expand.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/expand.o -MMD -MP -MF obj/expand.Td -c -o obj/expand.o src/expand/expand.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, + from src/bamToFastq/bamToFastq.h:15, + from src/bamToFastq/bamToFastq.cpp:15: +src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': +src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 32 | sam_hdr_write(fp, hdr); + | ~~~~~~~~~~~~~^~~~~~~~~ +In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/bamToBed/bamToBed.cpp:12: src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -600,14 +639,20 @@ g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/getOverlap.o -MMD -MP -MF obj/getOverlap.Td -c -o obj/getOverlap.o src/getOverlap/getOverlap.cpp * compiling src/groupBy/groupByHelp.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/groupByHelp.o -MMD -MP -MF obj/groupByHelp.Td -c -o obj/groupByHelp.o src/groupBy/groupByHelp.cpp -src/coverageFile/coverageFile.cpp: In member function 'virtual void CoverageFile::giveFinalReport(RecordOutputMgr*)': -src/coverageFile/coverageFile.cpp:100:11: warning: ignoring return value of 'int asprintf(char**, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 100 | asprintf(&depthPctString, "%0.7f", depthPct); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + * compiling src/groupBy/groupBy.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/groupBy.o -MMD -MP -MF obj/groupBy.Td -c -o obj/groupBy.o src/groupBy/groupBy.cpp + * compiling src/intersectFile/intersectHelp.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/intersectHelp.o -MMD -MP -MF obj/intersectHelp.Td -c -o obj/intersectHelp.o src/intersectFile/intersectHelp.cpp src/getOverlap/getOverlap.cpp: In function 'int getoverlap_main(int, char**)': src/getOverlap/getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable] 44 | bool haveColumns = false; | ^~~~~~~~~~~ + * compiling src/intersectFile/intersectFile.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/intersectFile.o -MMD -MP -MF obj/intersectFile.Td -c -o obj/intersectFile.o src/intersectFile/intersectFile.cpp +src/coverageFile/coverageFile.cpp: In member function 'virtual void CoverageFile::giveFinalReport(RecordOutputMgr*)': +src/coverageFile/coverageFile.cpp:100:11: warning: ignoring return value of 'int asprintf(char**, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 100 | asprintf(&depthPctString, "%0.7f", depthPct); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/coverageFile/coverageFile.cpp: In member function 'void CoverageFile::doMean(RecordOutputMgr*, RecordKeyVector&)': src/coverageFile/coverageFile.cpp:181:10: warning: ignoring return value of 'int asprintf(char**, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 181 | asprintf(&meanString, "%0.7f", mean); @@ -620,12 +665,6 @@ src/coverageFile/coverageFile.cpp:230:10: warning: ignoring return value of 'int asprintf(char**, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 230 | asprintf(&coveredFractionString, "%0.7f", coveredFraction); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - * compiling src/groupBy/groupBy.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/groupBy.o -MMD -MP -MF obj/groupBy.Td -c -o obj/groupBy.o src/groupBy/groupBy.cpp - * compiling src/intersectFile/intersectHelp.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/intersectHelp.o -MMD -MP -MF obj/intersectHelp.Td -c -o obj/intersectHelp.o src/intersectFile/intersectHelp.cpp - * compiling src/intersectFile/intersectFile.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/intersectFile.o -MMD -MP -MF obj/intersectFile.Td -c -o obj/intersectFile.o src/intersectFile/intersectFile.cpp * compiling src/fisher/fisherHelp.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fisherHelp.o -MMD -MP -MF obj/fisherHelp.Td -c -o obj/fisherHelp.o src/fisher/fisherHelp.cpp * compiling src/fisher/fisher.cpp @@ -634,14 +673,6 @@ g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/kfunc.o -MMD -MP -MF obj/kfunc.Td -c -o obj/kfunc.o src/fisher/kfunc.cpp * compiling src/jaccard/jaccardHelp.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/jaccardHelp.o -MMD -MP -MF obj/jaccardHelp.Td -c -o obj/jaccardHelp.o src/jaccard/jaccardHelp.cpp -In file included from src/utils/BamTools/include/api/BamReader.h:1, - from src/utils/GenomeFile/NewGenomeFile.h:20, - from src/genomeCoverageBed/genomeCoverageBed.h:13, - from src/genomeCoverageBed/genomeCoverageBed.cpp:13: -src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': -src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 32 | sam_hdr_write(fp, hdr); - | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/jaccard/jaccard.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/jaccard.o -MMD -MP -MF obj/jaccard.Td -c -o obj/jaccard.o src/jaccard/jaccard.cpp * compiling src/linksBed/linksMain.cpp @@ -660,6 +691,14 @@ g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/mergeHelp.o -MMD -MP -MF obj/mergeHelp.Td -c -o obj/mergeHelp.o src/mergeFile/mergeHelp.cpp * compiling src/mergeFile/mergeFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/mergeFile.o -MMD -MP -MF obj/mergeFile.Td -c -o obj/mergeFile.o src/mergeFile/mergeFile.cpp +In file included from src/utils/BamTools/include/api/BamReader.h:1, + from src/utils/GenomeFile/NewGenomeFile.h:20, + from src/genomeCoverageBed/genomeCoverageBed.h:13, + from src/genomeCoverageBed/genomeCoverageBed.cpp:13: +src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': +src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 32 | sam_hdr_write(fp, hdr); + | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/multiBamCov/multiBamCovMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiBamCovMain.o -MMD -MP -MF obj/multiBamCovMain.Td -c -o obj/multiBamCovMain.o src/multiBamCov/multiBamCovMain.cpp * compiling src/multiBamCov/multiBamCov.cpp @@ -667,8 +706,8 @@ * compiling src/multiIntersectBed/multiIntersectBedMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiIntersectBedMain.o -MMD -MP -MF obj/multiIntersectBedMain.Td -c -o obj/multiIntersectBedMain.o src/multiIntersectBed/multiIntersectBedMain.cpp * compiling src/multiIntersectBed/multiIntersectBed.cpp - * compiling src/nucBed/nucBedMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiIntersectBed.o -MMD -MP -MF obj/multiIntersectBed.Td -c -o obj/multiIntersectBed.o src/multiIntersectBed/multiIntersectBed.cpp + * compiling src/nucBed/nucBedMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/nucBedMain.o -MMD -MP -MF obj/nucBedMain.Td -c -o obj/nucBedMain.o src/nucBed/nucBedMain.cpp * compiling src/nucBed/nucBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/nucBed.o -MMD -MP -MF obj/nucBed.Td -c -o obj/nucBed.o src/nucBed/nucBed.cpp @@ -680,10 +719,6 @@ g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToPairMain.o -MMD -MP -MF obj/pairToPairMain.Td -c -o obj/pairToPairMain.o src/pairToPair/pairToPairMain.cpp * compiling src/pairToPair/pairToPair.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToPair.o -MMD -MP -MF obj/pairToPair.Td -c -o obj/pairToPair.o src/pairToPair/pairToPair.cpp - * compiling src/randomBed/randomBedMain.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/randomBedMain.o -MMD -MP -MF obj/randomBedMain.Td -c -o obj/randomBedMain.o src/randomBed/randomBedMain.cpp - * compiling src/randomBed/randomBed.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/randomBed.o -MMD -MP -MF obj/randomBed.Td -c -o obj/randomBed.o src/randomBed/randomBed.cpp src/multiBamCov/multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)': src/multiBamCov/multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable] 38 | bool haveBed = false; @@ -694,6 +729,18 @@ src/multiBamCov/multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] 47 | bool haveFraction = false; | ^~~~~~~~~~~~ + * compiling src/randomBed/randomBedMain.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/randomBedMain.o -MMD -MP -MF obj/randomBedMain.Td -c -o obj/randomBedMain.o src/randomBed/randomBedMain.cpp + * compiling src/randomBed/randomBed.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/randomBed.o -MMD -MP -MF obj/randomBed.Td -c -o obj/randomBed.o src/randomBed/randomBed.cpp +In file included from src/utils/BamTools/include/BamReader.hpp:4, + from src/utils/BamTools/include/api/BamMultiReader.h:4, + from src/multiBamCov/multiBamCov.h:16, + from src/multiBamCov/multiBamCov.cpp:13: +src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': +src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 32 | sam_hdr_write(fp, hdr); + | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/regressTest/regressTestMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/regressTestMain.o -MMD -MP -MF obj/regressTestMain.Td -c -o obj/regressTestMain.o src/regressTest/regressTestMain.cpp src/multiIntersectBed/multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)': @@ -706,24 +753,6 @@ src/multiIntersectBed/multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] 48 | bool haveFiller = true; | ^~~~~~~~~~ -In file included from src/utils/BamTools/include/BamReader.hpp:4, - from src/utils/BamTools/include/api/BamMultiReader.h:4, - from src/multiBamCov/multiBamCov.h:16, - from src/multiBamCov/multiBamCov.cpp:13: -src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': -src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 32 | sam_hdr_write(fp, hdr); - | ~~~~~~~~~~~~~^~~~~~~~~ - * compiling src/regressTest/RegressTest.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RegressTest.o -MMD -MP -MF obj/RegressTest.Td -c -o obj/RegressTest.o src/regressTest/RegressTest.cpp -src/pairToBed/pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector&, const string&)': -src/pairToBed/pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] - 257 | CHRPOS spanLength = 0; - | ^~~~~~~~~~ -src/pairToBed/pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)': -src/pairToBed/pairToBed.cpp:310:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] - 310 | CHRPOS spanLength = 0; - | ^~~~~~~~~~ src/pairToPair/pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)': src/pairToPair/pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] 44 | bool haveFraction = false; @@ -735,6 +764,8 @@ src/pairToPair/pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable] 113 | bool found2 = false; | ^~~~~~ + * compiling src/regressTest/RegressTest.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RegressTest.o -MMD -MP -MF obj/RegressTest.Td -c -o obj/RegressTest.o src/regressTest/RegressTest.cpp * compiling src/reldist/reldistMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/reldistMain.o -MMD -MP -MF obj/reldistMain.Td -c -o obj/reldistMain.o src/reldist/reldistMain.cpp src/pairToBed/pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)': @@ -743,15 +774,16 @@ | ^~~~~~~~~~~~ * compiling src/reldist/reldist.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/reldist.o -MMD -MP -MF obj/reldist.Td -c -o obj/reldist.o src/reldist/reldist.cpp -In file included from src/utils/BamTools/include/api/BamReader.h:1, - from src/pairToBed/pairToBed.h:15, - from src/pairToBed/pairToBed.cpp:13: -src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': -src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 32 | sam_hdr_write(fp, hdr); - | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/sampleFile/sampleHelp.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sampleHelp.o -MMD -MP -MF obj/sampleHelp.Td -c -o obj/sampleHelp.o src/sampleFile/sampleHelp.cpp +src/pairToBed/pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector&, const string&)': +src/pairToBed/pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] + 257 | CHRPOS spanLength = 0; + | ^~~~~~~~~~ +src/pairToBed/pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)': +src/pairToBed/pairToBed.cpp:310:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] + 310 | CHRPOS spanLength = 0; + | ^~~~~~~~~~ * compiling src/sampleFile/sampleFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sampleFile.o -MMD -MP -MF obj/sampleFile.Td -c -o obj/sampleFile.o src/sampleFile/sampleFile.cpp * compiling src/shiftBed/shiftBedMain.cpp @@ -760,18 +792,15 @@ g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shiftBed.o -MMD -MP -MF obj/shiftBed.Td -c -o obj/shiftBed.o src/shiftBed/shiftBed.cpp * compiling src/shuffleBed/shuffleBedMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shuffleBedMain.o -MMD -MP -MF obj/shuffleBedMain.Td -c -o obj/shuffleBedMain.o src/shuffleBed/shuffleBedMain.cpp +In file included from src/utils/BamTools/include/api/BamReader.h:1, + from src/pairToBed/pairToBed.h:15, + from src/pairToBed/pairToBed.cpp:13: +src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': +src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 32 | sam_hdr_write(fp, hdr); + | ~~~~~~~~~~~~~^~~~~~~~~ * compiling src/shuffleBed/shuffleBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shuffleBed.o -MMD -MP -MF obj/shuffleBed.Td -c -o obj/shuffleBed.o src/shuffleBed/shuffleBed.cpp - * compiling src/slopBed/slopBedMain.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/slopBedMain.o -MMD -MP -MF obj/slopBedMain.Td -c -o obj/slopBedMain.o src/slopBed/slopBedMain.cpp - * compiling src/slopBed/slopBed.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/slopBed.o -MMD -MP -MF obj/slopBed.Td -c -o obj/slopBed.o src/slopBed/slopBed.cpp - * compiling src/sortBed/sortMain.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sortMain.o -MMD -MP -MF obj/sortMain.Td -c -o obj/sortMain.o src/sortBed/sortMain.cpp -src/reldist/reldist.cpp: In member function 'void RelativeDistance::CalculateRelativeDistance()': -src/reldist/reldist.cpp:129:25: warning: comparison of integer expressions of different signedness: 'CHRPOS' {aka 'long int'} and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 129 | if (low_idx != chrom_mids->size() - 1) - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ src/regressTest/RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)': src/regressTest/RegressTest.cpp:431:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 431 | system(diffCmd.c_str()); @@ -784,6 +813,16 @@ src/regressTest/RegressTest.cpp:622:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 622 | fgets(sLine, 4192, fp); | ~~~~~^~~~~~~~~~~~~~~~~ + * compiling src/slopBed/slopBedMain.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/slopBedMain.o -MMD -MP -MF obj/slopBedMain.Td -c -o obj/slopBedMain.o src/slopBed/slopBedMain.cpp + * compiling src/slopBed/slopBed.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/slopBed.o -MMD -MP -MF obj/slopBed.Td -c -o obj/slopBed.o src/slopBed/slopBed.cpp + * compiling src/sortBed/sortMain.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sortMain.o -MMD -MP -MF obj/sortMain.Td -c -o obj/sortMain.o src/sortBed/sortMain.cpp +src/reldist/reldist.cpp: In member function 'void RelativeDistance::CalculateRelativeDistance()': +src/reldist/reldist.cpp:129:25: warning: comparison of integer expressions of different signedness: 'CHRPOS' {aka 'long int'} and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 129 | if (low_idx != chrom_mids->size() - 1) + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ * compiling src/sortBed/sortBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sortBed.o -MMD -MP -MF obj/sortBed.Td -c -o obj/sortBed.o src/sortBed/sortBed.cpp * compiling src/spacingFile/spacingHelp.cpp @@ -820,7 +859,6 @@ g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowMaker.o -MMD -MP -MF obj/windowMaker.Td -c -o obj/windowMaker.o src/windowMaker/windowMaker.cpp * compiling src/utils/FileRecordTools/FileRecordMgr.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileRecordMgr.o -MMD -MP -MF obj/FileRecordMgr.Td -c -o obj/FileRecordMgr.o src/utils/FileRecordTools/FileRecordMgr.cpp - * compiling src/utils/FileRecordTools/FileRecordMergeMgr.cpp src/unionBedGraphs/unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)': src/unionBedGraphs/unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable] 46 | bool haveFiles = false; @@ -831,9 +869,8 @@ src/unionBedGraphs/unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] 49 | bool haveFiller = true; | ^~~~~~~~~~ + * compiling src/utils/FileRecordTools/FileRecordMergeMgr.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileRecordMergeMgr.o -MMD -MP -MF obj/FileRecordMergeMgr.Td -c -o obj/FileRecordMergeMgr.o src/utils/FileRecordTools/FileRecordMergeMgr.cpp - * compiling src/utils/FileRecordTools/FileReaders/FileReader.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileReader.o -MMD -MP -MF obj/FileReader.Td -c -o obj/FileReader.o src/utils/FileRecordTools/FileReaders/FileReader.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/tagBam/tagBam.h:17, from src/tagBam/tagBam.cpp:13: @@ -841,10 +878,9 @@ src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ + * compiling src/utils/FileRecordTools/FileReaders/FileReader.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileReader.o -MMD -MP -MF obj/FileReader.Td -c -o obj/FileReader.o src/utils/FileRecordTools/FileReaders/FileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/SingleLineDelimTextFileReader.o -MMD -MP -MF obj/SingleLineDelimTextFileReader.Td -c -o obj/SingleLineDelimTextFileReader.o src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp - * compiling src/utils/FileRecordTools/FileReaders/BamFileReader.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BamFileReader.o -MMD -MP -MF obj/BamFileReader.Td -c -o obj/BamFileReader.o src/utils/FileRecordTools/FileReaders/BamFileReader.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/windowBed/windowBed.h:15, from src/windowBed/windowBed.cpp:13: @@ -852,6 +888,9 @@ src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/SingleLineDelimTextFileReader.o -MMD -MP -MF obj/SingleLineDelimTextFileReader.Td -c -o obj/SingleLineDelimTextFileReader.o src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp + * compiling src/utils/FileRecordTools/FileReaders/BamFileReader.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BamFileReader.o -MMD -MP -MF obj/BamFileReader.Td -c -o obj/BamFileReader.o src/utils/FileRecordTools/FileReaders/BamFileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BufferedStreamMgr.o -MMD -MP -MF obj/BufferedStreamMgr.Td -c -o obj/BufferedStreamMgr.o src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp * compiling src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp @@ -864,6 +903,10 @@ g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed3Interval.o -MMD -MP -MF obj/Bed3Interval.Td -c -o obj/Bed3Interval.o src/utils/FileRecordTools/Records/Bed3Interval.cpp * compiling src/utils/FileRecordTools/Records/Bed4Interval.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed4Interval.o -MMD -MP -MF obj/Bed4Interval.Td -c -o obj/Bed4Interval.o src/utils/FileRecordTools/Records/Bed4Interval.cpp +src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp: In member function 'bool BufferedStreamMgr::readFileChunk()': +src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:148:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 148 | if (_mainBufCurrLen < _useBufSize) { + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ * compiling src/utils/FileRecordTools/Records/BedGraphInterval.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BedGraphInterval.o -MMD -MP -MF obj/BedGraphInterval.Td -c -o obj/BedGraphInterval.o src/utils/FileRecordTools/Records/BedGraphInterval.cpp * compiling src/utils/FileRecordTools/Records/Bed5Interval.cpp @@ -872,13 +915,6 @@ g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed6Interval.o -MMD -MP -MF obj/Bed6Interval.Td -c -o obj/Bed6Interval.o src/utils/FileRecordTools/Records/Bed6Interval.cpp * compiling src/utils/FileRecordTools/Records/PlusFields.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/PlusFields.o -MMD -MP -MF obj/PlusFields.Td -c -o obj/PlusFields.o src/utils/FileRecordTools/Records/PlusFields.cpp -src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp: In member function 'bool BufferedStreamMgr::readFileChunk()': -src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:148:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 148 | if (_mainBufCurrLen < _useBufSize) { - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ - * compiling src/utils/FileRecordTools/Records/GffRecord.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/GffRecord.o -MMD -MP -MF obj/GffRecord.Td -c -o obj/GffRecord.o src/utils/FileRecordTools/Records/GffRecord.cpp - * compiling src/utils/FileRecordTools/Records/GffPlusRecord.cpp In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/utils/FileRecordTools/FileReaders/InputStreamMgr.h:14, from src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:8: @@ -886,6 +922,9 @@ src/utils/BamTools/include/SamHeader.hpp:32:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | sam_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ + * compiling src/utils/FileRecordTools/Records/GffRecord.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/GffRecord.o -MMD -MP -MF obj/GffRecord.Td -c -o obj/GffRecord.o src/utils/FileRecordTools/Records/GffRecord.cpp + * compiling src/utils/FileRecordTools/Records/GffPlusRecord.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/GffPlusRecord.o -MMD -MP -MF obj/GffPlusRecord.Td -c -o obj/GffPlusRecord.o src/utils/FileRecordTools/Records/GffPlusRecord.cpp * compiling src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/NoPosPlusRecord.o -MMD -MP -MF obj/NoPosPlusRecord.Td -c -o obj/NoPosPlusRecord.o src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp @@ -906,22 +945,22 @@ * compiling src/utils/FileRecordTools/Records/RecordList.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordList.o -MMD -MP -MF obj/RecordList.Td -c -o obj/RecordList.o src/utils/FileRecordTools/Records/RecordList.cpp * compiling src/utils/FileRecordTools/Records/RecordKeyList.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordKeyList.o -MMD -MP -MF obj/RecordKeyList.Td -c -o obj/RecordKeyList.o src/utils/FileRecordTools/Records/RecordKeyList.cpp * compiling src/utils/FileRecordTools/Records/RecordKeyVector.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordKeyList.o -MMD -MP -MF obj/RecordKeyList.Td -c -o obj/RecordKeyList.o src/utils/FileRecordTools/Records/RecordKeyList.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordKeyVector.o -MMD -MP -MF obj/RecordKeyVector.Td -c -o obj/RecordKeyVector.o src/utils/FileRecordTools/Records/RecordKeyVector.cpp * compiling src/utils/bedFile/bedFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedFile.o -MMD -MP -MF obj/bedFile.Td -c -o obj/bedFile.o src/utils/bedFile/bedFile.cpp +src/utils/FileRecordTools/Records/BlockMgr.cpp: In member function 'int BlockMgr::getNonRedundantOverlap()': +src/utils/FileRecordTools/Records/BlockMgr.cpp:194:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 194 | for (int i = 1; i < _overlapStarts.size(); ++i) + | ~~^~~~~~~~~~~~~~~~~~~~~~~ * compiling src/utils/BinTree/BinTree.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BinTree.o -MMD -MP -MF obj/BinTree.Td -c -o obj/BinTree.o src/utils/BinTree/BinTree.cpp * compiling src/utils/version/version.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/version.o -MMD -MP -MF obj/version.Td -c -o obj/version.o src/utils/version/version.cpp * compiling src/utils/bedGraphFile/bedGraphFile.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedGraphFile.o -MMD -MP -MF obj/bedGraphFile.Td -c -o obj/bedGraphFile.o src/utils/bedGraphFile/bedGraphFile.cpp -src/utils/FileRecordTools/Records/BlockMgr.cpp: In member function 'int BlockMgr::getNonRedundantOverlap()': -src/utils/FileRecordTools/Records/BlockMgr.cpp:194:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 194 | for (int i = 1; i < _overlapStarts.size(); ++i) - | ~~^~~~~~~~~~~~~~~~~~~~~~~ * compiling src/utils/chromsweep/chromsweep.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedGraphFile.o -MMD -MP -MF obj/bedGraphFile.Td -c -o obj/bedGraphFile.o src/utils/bedGraphFile/bedGraphFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/chromsweep.o -MMD -MP -MF obj/chromsweep.Td -c -o obj/chromsweep.o src/utils/chromsweep/chromsweep.cpp * compiling src/utils/Contexts/ContextBase.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextBase.o -MMD -MP -MF obj/ContextBase.Td -c -o obj/ContextBase.o src/utils/Contexts/ContextBase.cpp @@ -990,22 +1029,20 @@ g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BlockedIntervals.o -MMD -MP -MF obj/BlockedIntervals.Td -c -o obj/BlockedIntervals.o src/utils/BlockedIntervals/BlockedIntervals.cpp * compiling src/utils/Fasta/Fasta.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Fasta.o -MMD -MP -MF obj/Fasta.Td -c -o obj/Fasta.o src/utils/Fasta/Fasta.cpp - * compiling src/utils/Fasta/split.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/split.o -MMD -MP -MF obj/split.Td -c -o obj/split.o src/utils/Fasta/split.cpp - * compiling src/utils/VectorOps/VectorOps.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/VectorOps.o -MMD -MP -MF obj/VectorOps.Td -c -o obj/VectorOps.o src/utils/VectorOps/VectorOps.cpp src/utils/fileType/FileRecordTypeChecker.cpp: In member function 'bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)': src/utils/fileType/FileRecordTypeChecker.cpp:366:19: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 366 | for (int j=0; j < len; j++) { | ~~^~~~~ + * compiling src/utils/Fasta/split.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/split.o -MMD -MP -MF obj/split.Td -c -o obj/split.o src/utils/Fasta/split.cpp + * compiling src/utils/VectorOps/VectorOps.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/VectorOps.o -MMD -MP -MF obj/VectorOps.Td -c -o obj/VectorOps.o src/utils/VectorOps/VectorOps.cpp * compiling src/utils/GenomeFile/NewGenomeFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/NewGenomeFile.o -MMD -MP -MF obj/NewGenomeFile.Td -c -o obj/NewGenomeFile.o src/utils/GenomeFile/NewGenomeFile.cpp * compiling src/utils/GenomeFile/GenomeFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/GenomeFile.o -MMD -MP -MF obj/GenomeFile.Td -c -o obj/GenomeFile.o src/utils/GenomeFile/GenomeFile.cpp * compiling src/utils/RecordOutputMgr/RecordOutputMgr.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordOutputMgr.o -MMD -MP -MF obj/RecordOutputMgr.Td -c -o obj/RecordOutputMgr.o src/utils/RecordOutputMgr/RecordOutputMgr.cpp - * compiling src/utils/ToolBase/ToolBase.cpp -g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ToolBase.o -MMD -MP -MF obj/ToolBase.Td -c -o obj/ToolBase.o src/utils/ToolBase/ToolBase.cpp src/utils/Fasta/Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)': src/utils/Fasta/Fasta.cpp:292:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 292 | fread(seq, sizeof(char), seqlen, file); @@ -1014,6 +1051,8 @@ src/utils/Fasta/Fasta.cpp:334:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 334 | fread(seq, sizeof(char), (off_t) seqlen, file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + * compiling src/utils/ToolBase/ToolBase.cpp +g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ToolBase.o -MMD -MP -MF obj/ToolBase.Td -c -o obj/ToolBase.o src/utils/ToolBase/ToolBase.cpp src/utils/GenomeFile/GenomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()': src/utils/GenomeFile/GenomeFile.cpp:60:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable] 60 | long c2; @@ -1030,11 +1069,11 @@ g++ -g -Wall -O2 -std=c++11 -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6 -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BedtoolsDriver.o -MMD -MP -MF obj/BedtoolsDriver.Td -c -o obj/BedtoolsDriver.o src/utils/driver/BedtoolsDriver.cpp cd src/utils/htslib && make lib-static make[3]: Entering directory '/build/bedtools-2.30.0+dfsg/src/utils/htslib' -- Creating executables for old CLI. cc -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c -done. cc -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c +- Creating executables for old CLI. cc -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c +done. cc -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c cc -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c cc -g -O2 -fdebug-prefix-map=/build/bedtools-2.30.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c @@ -1089,7 +1128,7 @@ make[1]: Entering directory '/build/bedtools-2.30.0+dfsg' htsutil="../../bin/bedtools htsutil" \ dh_auto_test - make -j15 test + make -j16 test make[2]: Entering directory '/build/bedtools-2.30.0+dfsg' Testing bedtools bamtobed: bamtobed.t1...ok @@ -2006,7 +2045,7 @@ NB: the 'negativecontrol' test is supposed to fail. If it wasn't caught, something went wrong with this test script. make[2]: Leaving directory '/build/bedtools-2.30.0+dfsg' - rm -fr -- /tmp/dh-xdg-rundir-phC8uTJm + rm -fr -- /tmp/dh-xdg-rundir-sP3xV5bu make[1]: Leaving directory '/build/bedtools-2.30.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep @@ -2017,7 +2056,7 @@ make[1]: Entering directory '/build/bedtools-2.30.0+dfsg' dh_auto_install -- VERBOSE=1 install -d /build/bedtools-2.30.0\+dfsg/debian/tmp - make -j15 install DESTDIR=/build/bedtools-2.30.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" VERBOSE=1 + make -j16 install DESTDIR=/build/bedtools-2.30.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/bedtools-2.30.0+dfsg' mkdir -p /build/bedtools-2.30.0+dfsg/debian/tmp/usr/local/bin for file in bin/* ; do \ @@ -2062,27 +2101,27 @@ install -d debian/bedtools-test/usr/share/doc/bedtools-test install -p -m0644 debian/copyright debian/bedtools-test/usr/share/doc/bedtools-test/copyright dh_installchangelogs - install -p -m0644 debian/changelog debian/bedtools-test/usr/share/doc/bedtools-test/changelog.Debian install -p -m0644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian + install -p -m0644 debian/changelog debian/bedtools-test/usr/share/doc/bedtools-test/changelog.Debian dh_perl dh_link dh_strip_nondeterminism Using 1611764786 as canonical time Normalizing debian/bedtools-test/usr/share/bedtools/test/general/non-empty.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/data/aluY.chr1.bed.gz using File::StripNondeterminism::handlers::gzip - Normalizing debian/bedtools-test/usr/share/bedtools/data/refseq.chr1.exons.bed.gz using File::StripNondeterminism::handlers::gzip - Normalizing debian/bedtools-test/usr/share/bedtools/test/intersect/a_withLargeHeader_gzipped.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/data/simpleRepeats.chr1.bed.gz using File::StripNondeterminism::handlers::gzip - Normalizing debian/bedtools-test/usr/share/bedtools/test/bamtobed/extra-long-header.sam.gz using File::StripNondeterminism::handlers::gzip + Normalizing debian/bedtools-test/usr/share/bedtools/data/refseq.chr1.exons.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/test/intersect/a_gzipped.bed.gz using File::StripNondeterminism::handlers::gzip + Normalizing debian/bedtools-test/usr/share/bedtools/test/intersect/a_withLargeHeader_gzipped.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/data/gerp.chr1.bed.gz using File::StripNondeterminism::handlers::gzip + Normalizing debian/bedtools-test/usr/share/bedtools/test/bamtobed/extra-long-header.sam.gz using File::StripNondeterminism::handlers::gzip dh_compress cd debian/bedtools cd debian/bedtools-test - chmod a-x usr/share/doc/bedtools-test/changelog.Debian chmod a-x usr/share/doc/bedtools/changelog.Debian - gzip -9nf usr/share/doc/bedtools-test/changelog.Debian + chmod a-x usr/share/doc/bedtools-test/changelog.Debian gzip -9nf usr/share/doc/bedtools/changelog.Debian + gzip -9nf usr/share/doc/bedtools-test/changelog.Debian cd '/build/bedtools-2.30.0+dfsg' cd '/build/bedtools-2.30.0+dfsg' rm -f debian/bedtools-test.debhelper.log debian/bedtools.debhelper.log @@ -2142,12 +2181,12 @@ chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/bedtools-test/DEBIAN/md5sums dh_builddeb - dpkg-deb --root-owner-group --build debian/bedtools .. dpkg-deb --root-owner-group --build debian/.debhelper/bedtools/dbgsym-root .. dpkg-deb --root-owner-group --build debian/bedtools-test .. + dpkg-deb --root-owner-group --build debian/bedtools .. dpkg-deb: building package 'bedtools-test' in '../bedtools-test_2.30.0+dfsg-1_all.deb'. -dpkg-deb: building package 'bedtools' in '../bedtools_2.30.0+dfsg-1_amd64.deb'. dpkg-deb: building package 'bedtools-dbgsym' in '../bedtools-dbgsym_2.30.0+dfsg-1_amd64.deb'. +dpkg-deb: building package 'bedtools' in '../bedtools_2.30.0+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bedtools_2.30.0+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2156,12 +2195,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1785102/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1785102/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/3368056 and its subdirectories -I: Current time: Thu Jan 5 06:52:14 -12 2023 -I: pbuilder-time-stamp: 1672944734 +I: removing directory /srv/workspace/pbuilder/1785102 and its subdirectories +I: Current time: Thu Feb 8 15:19:42 +14 2024 +I: pbuilder-time-stamp: 1707355182