I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 15 13:37:28 +14 2026 I: pbuilder-time-stamp: 1768433848 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bedtools_2.31.1+dfsg-2.dsc] I: copying [./bedtools_2.31.1+dfsg.orig.tar.xz] I: copying [./bedtools_2.31.1+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Dec 4 19:20:23 2023 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bedtools_2.31.1+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting bedtools in bedtools-2.31.1+dfsg dpkg-source: info: unpacking bedtools_2.31.1+dfsg.orig.tar.xz dpkg-source: info: unpacking bedtools_2.31.1+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gzstream.h.patch dpkg-source: info: applying remove_barski_binding_site.png.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying hardening dpkg-source: info: applying htsutil dpkg-source: info: applying no_ulimit.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2932485/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-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 '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 14 23:37 /bin/sh -> /bin/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/2932485/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2932485/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=877be670b8194ac092902dd033b20574 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=2932485 PS4='+ ' 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.1E8RjI6L/pbuilderrc_hbJX --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1E8RjI6L/b2 --logfile b2/build.log bedtools_2.31.1+dfsg-2.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2932485/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), python3:any, zlib1g-dev, libbz2-dev, liblzma-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19965 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on python3:any. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbz2-dev{a} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libpipeline1{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 54 newly installed, 0 to remove and 0 not upgraded. Need to get 28.2 MB of archives. After unpacking 106 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.8-1 [815 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.8-1 [2163 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-4 [256 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2~rc1-2 [23.8 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.8-1 [1970 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.8-1 [677 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-6 [1184 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 44 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 28.2 MB in 0s (72.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19965 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.8-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.8-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-1_amd64.deb ... Unpacking python3.12-minimal (3.12.8-1) ... Setting up libpython3.12-minimal:amd64 (3.12.8-1) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-1) ... Selecting previously unselected package python3-minimal. (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 ... 20285 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.8-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.8-1_amd64.deb ... Unpacking python3.12 (3.12.8-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (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 ... 21348 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. 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Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up autoconf (2.72-3) ... Setting up liblzma-dev:amd64 (5.6.3-1+b1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2932485/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2932485/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/bedtools-2.31.1+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_2.31.1+dfsg-2_source.changes dpkg-buildpackage: info: source package bedtools dpkg-buildpackage: info: source version 2.31.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from bedtools-2.31.1+dfsg/debian/source/options: --single-debian-patch debian/rules clean dh clean dh_auto_clean make -j42 clean make[1]: Entering directory '/build/reproducible-path/bedtools-2.31.1+dfsg' * Cleaning up. make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[1]: Leaving directory '/build/reproducible-path/bedtools-2.31.1+dfsg' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/bedtools.substvars debian/bedtools-test.substvars debian/files rm -fr -- debian/bedtools/ debian/tmp/ debian/bedtools-test/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/bedtools-2.31.1+dfsg' dh_auto_build -- VERBOSE=1 make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/bedtools-2.31.1+dfsg' Building BEDTools: cd src/utils/htslib && make config.h ========================================================= make[3]: Entering directory '/build/reproducible-path/bedtools-2.31.1+dfsg/src/utils/htslib' DETECTED_VERSION = v2.31.1 CURRENT_VERSION = Updating version file. CXXFLAGS is [-g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection] * compiling src/bedtools.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-MMD -MP -MF obj/htsutil.Td -c -o obj/htsutil.o src/htsutil.cpp * compiling src/annotateBed/annotateBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/bamToBed/bamToBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/bamToFastq/bamToFastqMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-Wformat -Werror=format-security -fcf-protection -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 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-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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedToBam.o -MMD -MP -MF obj/bedToBam.Td -c -o obj/bedToBam.o src/bedToBam/bedToBam.cpp * compiling src/bedpeToBam/bedpeToBam.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed 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-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 -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 * compiling src/bedToIgv/bedToIgv.cpp * compiling src/bed12ToBed6/bed12ToBed6.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed 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-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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/closestFile/closestFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-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 echo '/* Default config.h generated by Makefile */' > config.h * compiling src/complementFile/complementFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-Isrc/utils/driver -Isrc/utils/BamTools -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 echo '#define HAVE_LIBBZ2 1' >> config.h * compiling src/coverageFile/coverageHelp.cpp * compiling src/coverageFile/coverageFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-Isrc/utils/BamTools -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 echo '#define HAVE_LIBLZMA 1' >> config.h g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/fastaFromBed/fastaFromBedMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fastaFromBedMain.o -MMD -MP -MF obj/fastaFromBedMain.Td -c -o obj/fastaFromBedMain.o src/fastaFromBed/fastaFromBedMain.cpp echo '#ifndef __APPLE__' >> config.h * compiling src/fastaFromBed/fastaFromBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fastaFromBed.o -MMD -MP -MF obj/fastaFromBed.Td -c -o obj/fastaFromBed.o src/fastaFromBed/fastaFromBed.cpp * compiling src/flankBed/flankBedMain.cpp echo '#define HAVE_LZMA_H 1' >> config.h * compiling src/genomeCoverageBed/genomeCoverageMain.cpp * compiling src/flankBed/flankBed.cpp * compiling src/genomeCoverageBed/genomeCoverageBed.cpp echo '#endif' >> config.h g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/flankBedMain.o -MMD -MP -MF obj/flankBedMain.Td -c -o obj/flankBedMain.o src/flankBed/flankBedMain.cpp echo '#define HAVE_FSEEKO 1' >> config.h g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/flankBed.o -MMD -MP -MF obj/flankBed.Td -c -o obj/flankBed.o src/flankBed/flankBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/genomeCoverageMain.o -MMD -MP -MF obj/genomeCoverageMain.Td -c -o obj/genomeCoverageMain.o src/genomeCoverageBed/genomeCoverageMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/genomeCoverageBed.o -MMD -MP -MF obj/genomeCoverageBed.Td -c -o obj/genomeCoverageBed.o src/genomeCoverageBed/genomeCoverageBed.cpp echo '#define HAVE_DRAND48 1' >> config.h * compiling src/getOverlap/getOverlap.cpp * compiling src/groupBy/groupByHelp.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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/groupBy.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 make[3]: Leaving directory '/build/reproducible-path/bedtools-2.31.1+dfsg/src/utils/htslib' g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/fisher/kfunc.cpp * compiling src/jaccard/jaccardHelp.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/mapFile.o -MMD -MP -MF obj/mapFile.Td -c -o obj/mapFile.o src/mapFile/mapFile.cpp * compiling src/mergeFile/mergeHelp.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/multiBamCov/multiBamCov.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/multiBamCov/multiBamCovMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/multiBamCov.o -MMD -MP -MF obj/multiBamCov.Td -c -o obj/multiBamCov.o src/multiBamCov/multiBamCov.cpp * compiling src/multiIntersectBed/multiIntersectBedMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 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/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; | ^~~~~~~~~~~ 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; | ^~~~~~~~~~~ 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/nucBed/nucBedMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/pairToBed/pairToBedMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToBedMain.o -MMD -MP -MF obj/pairToBedMain.Td -c -o obj/pairToBedMain.o src/pairToBed/pairToBedMain.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; | ^~~~~~~~~~~ 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:32:30: 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/pairToBed/pairToBed.cpp * compiling src/pairToPair/pairToPairMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/pairToBed.o -MMD -MP -MF obj/pairToBed.Td -c -o obj/pairToBed.o src/pairToBed/pairToBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 src/coverageFile/coverageFile.cpp: In member function 'virtual void CoverageFile::giveFinalReport(RecordOutputMgr*)': src/coverageFile/coverageFile.cpp:100:25: 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:181:17: warning: ignoring return value of 'int asprintf(char**, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 181 | asprintf(&meanString, "%0.7f", mean); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/coverageFile/coverageFile.cpp: In member function 'void CoverageFile::doHist(RecordOutputMgr*, RecordKeyVector&)': src/coverageFile/coverageFile.cpp:210:25: warning: ignoring return value of 'int asprintf(char**, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 210 | asprintf(&coveredFractionString, "%0.7f", coveredFraction); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/coverageFile/coverageFile.cpp: In member function 'void CoverageFile::doDefault(RecordOutputMgr*, RecordKeyVector&)': src/coverageFile/coverageFile.cpp:230:17: warning: ignoring return value of 'int asprintf(char**, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 230 | asprintf(&coveredFractionString, "%0.7f", coveredFraction); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:32:30: 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/pairToPair/pairToPair.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 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:32:30: 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/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; | ^~~~~~~ src/multiBamCov/multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable] 39 | bool haveBams = false; | ^~~~~~~~ src/multiBamCov/multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] 47 | bool haveFraction = false; | ^~~~~~~~~~~~ src/multiIntersectBed/multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)': src/multiIntersectBed/multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable] 45 | bool haveFiles = false; | ^~~~~~~~~ src/multiIntersectBed/multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable] 47 | bool haveGenome = false; | ^~~~~~~~~~ src/multiIntersectBed/multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] 48 | bool haveFiller = true; | ^~~~~~~~~~ * compiling src/randomBed/randomBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/regressTest/regressTestMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/regressTest/RegressTest.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/reldist/reldist.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/sampleFile/sampleHelp.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/sampleFile/sampleFile.cpp * compiling src/shiftBed/shiftBedMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/shiftBedMain.o -MMD -MP -MF obj/shiftBedMain.Td -c -o obj/shiftBedMain.o src/shiftBed/shiftBedMain.cpp * compiling src/shiftBed/shiftBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 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:32:30: 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/pairToBed/pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)': src/pairToBed/pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] 43 | bool haveFraction = false; | ^~~~~~~~~~~~ * compiling src/shuffleBed/shuffleBedMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/shuffleBed/shuffleBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 src/pairToPair/pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)': src/pairToPair/pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable] 112 | bool found1 = false; | ^~~~~~ src/pairToPair/pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable] 113 | bool found2 = false; | ^~~~~~ 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; | ^~~~~~~~~~~~ * compiling src/slopBed/slopBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/sortBed/sortBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/spacingHelp.o -MMD -MP -MF obj/spacingHelp.Td -c -o obj/spacingHelp.o src/spacingFile/spacingHelp.cpp * compiling src/spacingFile/spacingFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/spacingFile.o -MMD -MP -MF obj/spacingFile.Td -c -o obj/spacingFile.o src/spacingFile/spacingFile.cpp * compiling src/split/splitBedMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/splitBedMain.o -MMD -MP -MF obj/splitBedMain.Td -c -o obj/splitBedMain.o src/split/splitBedMain.cpp src/pairToBed/pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector&, const std::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 std::string&)': src/pairToBed/pairToBed.cpp:310:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] 310 | CHRPOS spanLength = 0; | ^~~~~~~~~~ * compiling src/split/splitBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/splitBed.o -MMD -MP -MF obj/splitBed.Td -c -o obj/splitBed.o src/split/splitBed.cpp * compiling src/subtractFile/subtractHelp.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/subtractHelp.o -MMD -MP -MF obj/subtractHelp.Td -c -o obj/subtractHelp.o src/subtractFile/subtractHelp.cpp * compiling src/subtractFile/subtractFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/subtractFile.o -MMD -MP -MF obj/subtractFile.Td -c -o obj/subtractFile.o src/subtractFile/subtractFile.cpp * compiling src/summaryFile/summaryHelp.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/summaryHelp.o -MMD -MP -MF obj/summaryHelp.Td -c -o obj/summaryHelp.o src/summaryFile/summaryHelp.cpp * compiling src/summaryFile/summaryFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/summaryFile.o -MMD -MP -MF obj/summaryFile.Td -c -o obj/summaryFile.o src/summaryFile/summaryFile.cpp * compiling src/tagBam/tagBamMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/tagBamMain.o -MMD -MP -MF obj/tagBamMain.Td -c -o obj/tagBamMain.o src/tagBam/tagBamMain.cpp * compiling src/tagBam/tagBam.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/tagBam.o -MMD -MP -MF obj/tagBam.Td -c -o obj/tagBam.o src/tagBam/tagBam.cpp * compiling src/unionBedGraphs/unionBedGraphsMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/unionBedGraphsMain.o -MMD -MP -MF obj/unionBedGraphsMain.Td -c -o obj/unionBedGraphsMain.o src/unionBedGraphs/unionBedGraphsMain.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:32:30: 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/unionBedGraphs/unionBedGraphs.cpp * compiling src/windowBed/windowMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowMain.o -MMD -MP -MF obj/windowMain.Td -c -o obj/windowMain.o src/windowBed/windowMain.cpp * compiling src/windowBed/windowBed.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/unionBedGraphs.o -MMD -MP -MF obj/unionBedGraphs.Td -c -o obj/unionBedGraphs.o src/unionBedGraphs/unionBedGraphs.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowBed.o -MMD -MP -MF obj/windowBed.Td -c -o obj/windowBed.o src/windowBed/windowBed.cpp * compiling src/windowMaker/windowMakerMain.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/windowMakerMain.o -MMD -MP -MF obj/windowMakerMain.Td -c -o obj/windowMakerMain.o src/windowMaker/windowMakerMain.cpp * compiling src/windowMaker/windowMaker.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 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:431:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 431 | system(diffCmd.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~ src/regressTest/RegressTest.cpp: In member function 'bool RegressTest::startMemoryProfile(bool)': src/regressTest/RegressTest.cpp:573:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 573 | fgets(sLine, 4192, fp); | ~~~~~^~~~~~~~~~~~~~~~~ src/regressTest/RegressTest.cpp: In member function 'bool RegressTest::calcMemoryStats()': src/regressTest/RegressTest.cpp:622:22: 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/utils/FileRecordTools/FileRecordMgr.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 In file included from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from src/utils/lineFileUtilities/lineFileUtilities.h:8, from src/genomeCoverageBed/genomeCoverageBed.cpp:12: In member function 'std::streamsize std::ios_base::precision(std::streamsize)', inlined from 'void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector&, const CHRPOS&, const std::string&)' at src/genomeCoverageBed/genomeCoverageBed.cpp:541:23: /usr/include/c++/14/bits/ios_base.h:764:20: warning: 'prec' may be used uninitialized [-Wmaybe-uninitialized] 764 | _M_precision = __prec; | ~~~~~~~~~~~~~^~~~~~~~ src/genomeCoverageBed/genomeCoverageBed.cpp: In member function 'void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector&, const CHRPOS&, const std::string&)': src/genomeCoverageBed/genomeCoverageBed.cpp:491:16: note: 'prec' was declared here 491 | streamsize prec; | ^~~~ In function 'constexpr std::_Ios_Fmtflags std::operator|(_Ios_Fmtflags, _Ios_Fmtflags)', inlined from 'const std::_Ios_Fmtflags& std::operator|=(_Ios_Fmtflags&, _Ios_Fmtflags)' at /usr/include/c++/14/bits/ios_base.h:105:22, inlined from 'std::ios_base::fmtflags std::ios_base::setf(fmtflags)' at /usr/include/c++/14/bits/ios_base.h:712:19, inlined from 'void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector&, const CHRPOS&, const std::string&)' at src/genomeCoverageBed/genomeCoverageBed.cpp:542:18: /usr/include/c++/14/bits/ios_base.h:90:71: warning: 'fflags' may be used uninitialized [-Wmaybe-uninitialized] 90 | { return _Ios_Fmtflags(static_cast(__a) | static_cast(__b)); } | ^ src/genomeCoverageBed/genomeCoverageBed.cpp: In member function 'void BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector&, const CHRPOS&, const std::string&)': src/genomeCoverageBed/genomeCoverageBed.cpp:492:29: note: 'fflags' was declared here 492 | std::ios_base::fmtflags fflags; | ^~~~~~ In member function 'std::streamsize std::ios_base::precision(std::streamsize)', inlined from 'void BedGenomeCoverage::ReportChromCoverage(const std::vector&, const CHRPOS&, const std::string&, chromHistMap&)' at src/genomeCoverageBed/genomeCoverageBed.cpp:401:27: /usr/include/c++/14/bits/ios_base.h:764:20: warning: 'prec' may be used uninitialized [-Wmaybe-uninitialized] 764 | _M_precision = __prec; | ~~~~~~~~~~~~~^~~~~~~~ src/genomeCoverageBed/genomeCoverageBed.cpp: In member function 'void BedGenomeCoverage::ReportChromCoverage(const std::vector&, const CHRPOS&, const std::string&, chromHistMap&)': src/genomeCoverageBed/genomeCoverageBed.cpp:381:20: note: 'prec' was declared here 381 | streamsize prec; | ^~~~ In function 'constexpr std::_Ios_Fmtflags std::operator|(_Ios_Fmtflags, _Ios_Fmtflags)', inlined from 'const std::_Ios_Fmtflags& std::operator|=(_Ios_Fmtflags&, _Ios_Fmtflags)' at /usr/include/c++/14/bits/ios_base.h:105:22, inlined from 'std::ios_base::fmtflags std::ios_base::setf(fmtflags)' at /usr/include/c++/14/bits/ios_base.h:712:19, inlined from 'void BedGenomeCoverage::ReportChromCoverage(const std::vector&, const CHRPOS&, const std::string&, chromHistMap&)' at src/genomeCoverageBed/genomeCoverageBed.cpp:402:22: /usr/include/c++/14/bits/ios_base.h:90:71: warning: 'fflags' may be used uninitialized [-Wmaybe-uninitialized] 90 | { return _Ios_Fmtflags(static_cast(__a) | static_cast(__b)); } | ^ src/genomeCoverageBed/genomeCoverageBed.cpp: In member function 'void BedGenomeCoverage::ReportChromCoverage(const std::vector&, const CHRPOS&, const std::string&, chromHistMap&)': src/genomeCoverageBed/genomeCoverageBed.cpp:382:33: note: 'fflags' was declared here 382 | std::ios_base::fmtflags fflags; | ^~~~~~ * compiling src/utils/FileRecordTools/FileReaders/FileReader.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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/InputStreamMgr.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/InputStreamMgr.o -MMD -MP -MF obj/InputStreamMgr.Td -c -o obj/InputStreamMgr.o src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp * compiling src/utils/FileRecordTools/Records/Record.cpp * compiling src/utils/FileRecordTools/Records/EmptyRecord.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Record.o -MMD -MP -MF obj/Record.Td -c -o obj/Record.o src/utils/FileRecordTools/Records/Record.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/EmptyRecord.o -MMD -MP -MF obj/EmptyRecord.Td -c -o obj/EmptyRecord.o src/utils/FileRecordTools/Records/EmptyRecord.cpp * compiling src/utils/FileRecordTools/Records/Bed3Interval.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 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; | ^~~~~~~~~ src/unionBedGraphs/unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable] 48 | bool haveGenome = false; | ^~~~~~~~~~ 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/Records/Bed4Interval.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/utils/FileRecordTools/Records/BedGraphInterval.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 In file included from src/utils/BamTools/include/api/BamReader.h:1, from src/tagBam/tagBam.h:17, from src/tagBam/tagBam.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:32:30: 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/Bed5Interval.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed5Interval.o -MMD -MP -MF obj/Bed5Interval.Td -c -o obj/Bed5Interval.o src/utils/FileRecordTools/Records/Bed5Interval.cpp * compiling src/utils/FileRecordTools/Records/Bed6Interval.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/utils/FileRecordTools/Records/GffRecord.cpp * compiling src/utils/FileRecordTools/Records/GffPlusRecord.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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/NoPosPlusRecord.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/utils/FileRecordTools/Records/BedPlusInterval.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BedPlusInterval.o -MMD -MP -MF obj/BedPlusInterval.Td -c -o obj/BedPlusInterval.o src/utils/FileRecordTools/Records/BedPlusInterval.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: src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': src/utils/BamTools/include/SamHeader.hpp:32:30: 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/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp: In member function 'bool BufferedStreamMgr::readFileChunk()': src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:148:37: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 148 | if (_mainBufCurrLen < _useBufSize) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 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: src/utils/BamTools/include/SamHeader.hpp: In function 'int htslib_future::sam_hdr_rebuild(bam_hdr_t*)': src/utils/BamTools/include/SamHeader.hpp:32:30: 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/Bed12Interval.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Bed12Interval.o -MMD -MP -MF obj/Bed12Interval.Td -c -o obj/Bed12Interval.o src/utils/FileRecordTools/Records/Bed12Interval.cpp * compiling src/utils/FileRecordTools/Records/BamRecord.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BamRecord.o -MMD -MP -MF obj/BamRecord.Td -c -o obj/BamRecord.o src/utils/FileRecordTools/Records/BamRecord.cpp * compiling src/utils/FileRecordTools/Records/VcfRecord.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/VcfRecord.o -MMD -MP -MF obj/VcfRecord.Td -c -o obj/VcfRecord.o src/utils/FileRecordTools/Records/VcfRecord.cpp * compiling src/utils/FileRecordTools/Records/BlockMgr.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BlockMgr.o -MMD -MP -MF obj/BlockMgr.Td -c -o obj/BlockMgr.o src/utils/FileRecordTools/Records/BlockMgr.cpp * compiling src/utils/FileRecordTools/Records/StrandQueue.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/StrandQueue.o -MMD -MP -MF obj/StrandQueue.Td -c -o obj/StrandQueue.o src/utils/FileRecordTools/Records/StrandQueue.cpp * compiling src/utils/FileRecordTools/Records/RecordMgr.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/RecordMgr.o -MMD -MP -MF obj/RecordMgr.Td -c -o obj/RecordMgr.o src/utils/FileRecordTools/Records/RecordMgr.cpp * compiling src/utils/FileRecordTools/Records/RecordList.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/utils/BinTree/BinTree.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/utils/chromsweep/chromsweep.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/utils/Contexts/ContextIntersect.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextIntersect.o -MMD -MP -MF obj/ContextIntersect.Td -c -o obj/ContextIntersect.o src/utils/Contexts/ContextIntersect.cpp * compiling src/utils/Contexts/ContextFisher.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextFisher.o -MMD -MP -MF obj/ContextFisher.Td -c -o obj/ContextFisher.o src/utils/Contexts/ContextFisher.cpp * compiling src/utils/Contexts/ContextMap.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextMap.o -MMD -MP -MF obj/ContextMap.Td -c -o obj/ContextMap.o src/utils/Contexts/ContextMap.cpp * compiling src/utils/Contexts/ContextSample.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSample.o -MMD -MP -MF obj/ContextSample.Td -c -o obj/ContextSample.o src/utils/Contexts/ContextSample.cpp * compiling src/utils/Contexts/ContextSpacing.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSpacing.o -MMD -MP -MF obj/ContextSpacing.Td -c -o obj/ContextSpacing.o src/utils/Contexts/ContextSpacing.cpp * compiling src/utils/Contexts/ContextMerge.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextMerge.o -MMD -MP -MF obj/ContextMerge.Td -c -o obj/ContextMerge.o src/utils/Contexts/ContextMerge.cpp * compiling src/utils/Contexts/ContextJaccard.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextJaccard.o -MMD -MP -MF obj/ContextJaccard.Td -c -o obj/ContextJaccard.o src/utils/Contexts/ContextJaccard.cpp src/utils/FileRecordTools/Records/BlockMgr.cpp: In member function 'int BlockMgr::getNonRedundantOverlap()': src/utils/FileRecordTools/Records/BlockMgr.cpp:194:35: 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/Contexts/ContextClosest.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextClosest.o -MMD -MP -MF obj/ContextClosest.Td -c -o obj/ContextClosest.o src/utils/Contexts/ContextClosest.cpp * compiling src/utils/Contexts/ContextSubtract.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSubtract.o -MMD -MP -MF obj/ContextSubtract.Td -c -o obj/ContextSubtract.o src/utils/Contexts/ContextSubtract.cpp * compiling src/utils/Contexts/ContextCoverage.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextCoverage.o -MMD -MP -MF obj/ContextCoverage.Td -c -o obj/ContextCoverage.o src/utils/Contexts/ContextCoverage.cpp * compiling src/utils/Contexts/ContextComplement.cpp * compiling src/utils/Contexts/ContextGroupBy.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextComplement.o -MMD -MP -MF obj/ContextComplement.Td -c -o obj/ContextComplement.o src/utils/Contexts/ContextComplement.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextGroupBy.o -MMD -MP -MF obj/ContextGroupBy.Td -c -o obj/ContextGroupBy.o src/utils/Contexts/ContextGroupBy.cpp * compiling src/utils/Contexts/ContextSummary.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ContextSummary.o -MMD -MP -MF obj/ContextSummary.Td -c -o obj/ContextSummary.o src/utils/Contexts/ContextSummary.cpp * compiling src/utils/general/ParseTools.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ParseTools.o -MMD -MP -MF obj/ParseTools.Td -c -o obj/ParseTools.o src/utils/general/ParseTools.cpp * compiling src/utils/general/PushBackStreamBuf.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/PushBackStreamBuf.o -MMD -MP -MF obj/PushBackStreamBuf.Td -c -o obj/PushBackStreamBuf.o src/utils/general/PushBackStreamBuf.cpp * compiling src/utils/general/CompressionTools.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/CompressionTools.o -MMD -MP -MF obj/CompressionTools.Td -c -o obj/CompressionTools.o src/utils/general/CompressionTools.cpp * compiling src/utils/general/Tokenizer.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Tokenizer.o -MMD -MP -MF obj/Tokenizer.Td -c -o obj/Tokenizer.o src/utils/general/Tokenizer.cpp * compiling src/utils/general/CommonHelp.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/CommonHelp.o -MMD -MP -MF obj/CommonHelp.Td -c -o obj/CommonHelp.o src/utils/general/CommonHelp.cpp * compiling src/utils/general/ErrorMsg.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/ErrorMsg.o -MMD -MP -MF obj/ErrorMsg.Td -c -o obj/ErrorMsg.o src/utils/general/ErrorMsg.cpp * compiling src/utils/general/Random.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/Random.o -MMD -MP -MF obj/Random.Td -c -o obj/Random.o src/utils/general/Random.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Isrc/utils/gzstream -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/gzstream.o src/utils/gzstream/gzstream.C * compiling src/utils/fileType/fileType.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/fileType.o -MMD -MP -MF obj/fileType.Td -c -o obj/fileType.o src/utils/fileType/fileType.cpp * compiling src/utils/fileType/FileRecordTypeChecker.cpp * compiling src/utils/bedFilePE/bedFilePE.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/FileRecordTypeChecker.o -MMD -MP -MF obj/FileRecordTypeChecker.Td -c -o obj/FileRecordTypeChecker.o src/utils/fileType/FileRecordTypeChecker.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/bedFilePE.o -MMD -MP -MF obj/bedFilePE.Td -c -o obj/bedFilePE.o src/utils/bedFilePE/bedFilePE.cpp * compiling src/utils/KeyListOps/KeyListOps.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/KeyListOps.o -MMD -MP -MF obj/KeyListOps.Td -c -o obj/KeyListOps.o src/utils/KeyListOps/KeyListOps.cpp * compiling src/utils/KeyListOps/KeyListOpsMethods.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/KeyListOpsMethods.o -MMD -MP -MF obj/KeyListOpsMethods.Td -c -o obj/KeyListOpsMethods.o src/utils/KeyListOps/KeyListOpsMethods.cpp * compiling src/utils/NewChromsweep/NewChromsweep.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/NewChromsweep.o -MMD -MP -MF obj/NewChromsweep.Td -c -o obj/NewChromsweep.o src/utils/NewChromsweep/NewChromsweep.cpp * compiling src/utils/NewChromsweep/CloseSweep.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/CloseSweep.o -MMD -MP -MF obj/CloseSweep.Td -c -o obj/CloseSweep.o src/utils/NewChromsweep/CloseSweep.cpp * compiling src/utils/sequenceUtilities/sequenceUtils.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/sequenceUtils.o -MMD -MP -MF obj/sequenceUtils.Td -c -o obj/sequenceUtils.o src/utils/sequenceUtilities/sequenceUtils.cpp * compiling src/utils/tabFile/tabFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/tabFile.o -MMD -MP -MF obj/tabFile.Td -c -o obj/tabFile.o src/utils/tabFile/tabFile.cpp * compiling src/utils/BamTools-Ancillary/BamAncillary.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2 -MT obj/BamAncillary.o -MMD -MP -MF obj/BamAncillary.Td -c -o obj/BamAncillary.o src/utils/BamTools-Ancillary/BamAncillary.cpp * compiling src/utils/BlockedIntervals/BlockedIntervals.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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/GenomeFile/NewGenomeFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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/VectorOps/VectorOps.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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/GenomeFile.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 * compiling src/utils/driver/BedtoolsDriver.cpp g++ -g -Wall -O2 -std=c++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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/reproducible-path/bedtools-2.31.1+dfsg/src/utils/htslib' - Creating executables for old CLI. cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c done. cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c src/utils/fileType/FileRecordTypeChecker.cpp: In member function 'bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)': src/utils/fileType/FileRecordTypeChecker.cpp:366:33: 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++) { | ~~^~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.9"' > version.h cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c 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; | ^~ src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function 'void RecordOutputMgr::printClosest(RecordKeyVector&, const std::vector*)': src/utils/RecordOutputMgr/RecordOutputMgr.cpp:170:56: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 170 | if (context->getNumClosestHitsWanted() > keyList.size()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ src/utils/RecordOutputMgr/RecordOutputMgr.cpp: In member function 'void RecordOutputMgr::reportOverlapSummary(RecordKeyVector&)': src/utils/RecordOutputMgr/RecordOutputMgr.cpp:456:38: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 456 | for (size_t i = 0; i < _context->getNumInputFiles(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/files.o cram/files.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/rANS_static.o cram/rANS_static.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/sam_header.o cram/sam_header.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o ranlib libhts.a make[3]: Leaving directory '/build/reproducible-path/bedtools-2.31.1+dfsg/src/utils/htslib' - Building main bedtools binary. g++ -Wl,-z,relro -Wl,-z,now -o bin/bedtools obj/bedtools.o obj/htsutil.o obj/annotateMain.o obj/annotateBed.o obj/bamToBed.o obj/bamToFastqMain.o obj/bamToFastq.o obj/bedToBam.o obj/bedpeToBam.o obj/bedToIgv.o obj/bed12ToBed6.o obj/closestHelp.o obj/closestFile.o obj/clusterMain.o obj/clusterBed.o obj/complementHelp.o obj/complementFile.o obj/coverageHelp.o obj/coverageFile.o obj/expand.o obj/fastaFromBedMain.o obj/fastaFromBed.o obj/flankBedMain.o obj/flankBed.o obj/genomeCoverageMain.o obj/genomeCoverageBed.o obj/getOverlap.o obj/groupByHelp.o obj/groupBy.o obj/intersectHelp.o obj/intersectFile.o obj/fisherHelp.o obj/fisher.o obj/kfunc.o obj/jaccardHelp.o obj/jaccard.o obj/linksMain.o obj/linksBed.o obj/maskFastaFromBedMain.o obj/maskFastaFromBed.o obj/mapHelp.o obj/mapFile.o obj/mergeHelp.o obj/mergeFile.o obj/multiBamCovMain.o obj/multiBamCov.o obj/multiIntersectBedMain.o obj/multiIntersectBed.o obj/nucBedMain.o obj/nucBed.o obj/pairToBedMain.o obj/pairToBed.o obj/pairToPairMain.o obj/pairToPair.o obj/randomBedMain.o obj/randomBed.o obj/regressTestMain.o obj/RegressTest.o obj/reldistMain.o obj/reldist.o obj/sampleHelp.o obj/sampleFile.o obj/shiftBedMain.o obj/shiftBed.o obj/shuffleBedMain.o obj/shuffleBed.o obj/slopBedMain.o obj/slopBed.o obj/sortMain.o obj/sortBed.o obj/spacingHelp.o obj/spacingFile.o obj/splitBedMain.o obj/splitBed.o obj/subtractHelp.o obj/subtractFile.o obj/summaryHelp.o obj/summaryFile.o obj/tagBamMain.o obj/tagBam.o obj/unionBedGraphsMain.o obj/unionBedGraphs.o obj/windowMain.o obj/windowBed.o obj/windowMakerMain.o obj/windowMaker.o obj/FileRecordMgr.o obj/FileRecordMergeMgr.o obj/FileReader.o obj/SingleLineDelimTextFileReader.o obj/BamFileReader.o obj/BufferedStreamMgr.o obj/InputStreamMgr.o obj/Record.o obj/EmptyRecord.o obj/Bed3Interval.o obj/Bed4Interval.o obj/BedGraphInterval.o obj/Bed5Interval.o obj/Bed6Interval.o obj/PlusFields.o obj/GffRecord.o obj/GffPlusRecord.o obj/NoPosPlusRecord.o obj/BedPlusInterval.o obj/Bed12Interval.o obj/BamRecord.o obj/VcfRecord.o obj/BlockMgr.o obj/StrandQueue.o obj/RecordMgr.o obj/RecordList.o obj/RecordKeyList.o obj/RecordKeyVector.o obj/bedFile.o obj/BinTree.o obj/version.o obj/bedGraphFile.o obj/chromsweep.o obj/ContextBase.o obj/ContextIntersect.o obj/ContextFisher.o obj/ContextMap.o obj/ContextSample.o obj/ContextSpacing.o obj/ContextMerge.o obj/ContextJaccard.o obj/ContextClosest.o obj/ContextSubtract.o obj/ContextCoverage.o obj/ContextComplement.o obj/ContextGroupBy.o obj/ContextSummary.o obj/ParseTools.o obj/PushBackStreamBuf.o obj/CompressionTools.o obj/Tokenizer.o obj/CommonHelp.o obj/ErrorMsg.o obj/Random.o obj/gzstream.o obj/fileType.o obj/FileRecordTypeChecker.o obj/bedFilePE.o obj/KeyListOps.o obj/KeyListOpsMethods.o obj/NewChromsweep.o obj/CloseSweep.o obj/sequenceUtils.o obj/tabFile.o obj/BamAncillary.o obj/BlockedIntervals.o obj/Fasta.o obj/split.o obj/VectorOps.o obj/NewGenomeFile.o obj/GenomeFile.o obj/RecordOutputMgr.o obj/ToolBase.o obj/BedtoolsDriver.o src/utils/htslib/libhts.a -lz -lm -lbz2 -llzma -lpthread done. make[2]: Leaving directory '/build/reproducible-path/bedtools-2.31.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/bedtools-2.31.1+dfsg' rm -f debian/bedtools-test.debhelper.log debian/bedtools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/bedtools-2.31.1+dfsg' htsutil="../../bin/bedtools htsutil" \ dh_auto_test make -j42 test make[2]: Entering directory '/build/reproducible-path/bedtools-2.31.1+dfsg' Testing bedtools bamtobed: bamtobed.t1...ok bamtobed.t2...ok bamtobed.t3...ok bamtobed.t4...ok bamtobed.t5...ok bamtobed.t6...ok bamtobed.t7...ok bamtobed.t8...ok bamtobed.t9...ok bamtobed.t10...ok bamtobed.t9...ok bamtobed.t11...ok bamtobed.t12..ok bamtobed.t13..ok Testing bedtools bamtofastq: ok ok Testing bedtools bed12tobed6: bed12tobed6.t1...ok bed12tobed6.t2...ok bed12tobed6.t3...ok bed12tobed6.t4...ok bed12tobed6.t5...ok Testing bedtools bedtobam: bedtobam.t1...ok Testing bedtools bigchroms: bigchroms.t01...ok bigchroms.t02...ok bigchroms.t03... skip set env var 'BT_NO_BIG_FILES' to run this test bigchroms.t04... merge ok bigchroms.t05... closest ok Testing bedtools closest: closest.t1...ok closest.t2...ok closest.t3...ok closest.t4...ok closest.t5...ok closest.t6...ok closest.t7...ok closest.t8...ok closest.t9...ok closest.t10...ok closest.t11...ok closest.t13...ok closest.t14...ok closest.t15...ok closest.t16...ok closest.t17...ok closest.t18...ok closest.t19...ok closest.t20...ok closest.t21...ok closest.t22...ok closest.t23...ok closest.t24...ok closest.t25...ok closest.t26...ok closest.t27...ok closest.t28...ok closest.t29...ok closest.t30...ok closest.t31...ok closest.t32...ok closest.t33...ok closest.t34...ok closest.t35...ok closest.t36...ok closest.t37...ok closest.t38...ok closest.t39...ok closest.t40...ok closest.t41...ok closest.t42...ok closest.t43...ok closest.t44...ok closest.t45...ok closest.t46...ok closest.t47...ok closest.t48...ok closest.t49...ok closest.t50...ok closest.t51...ok closest.t52...ok closest.t53...ok closest.t54...ok closest.t55...ok closest.t56...ok closest.t57...ok closest.t58...ok closest.t59...ok closest.t60...ok closest.t61...ok closest.t62...ok closest.t63...ok closest.t64...ok closest.t65...ok closest.t66...ok closest.t67...ok closest.t68...ok closest.t69...ok closest.t70...ok closest.t71...ok ########################################################### # # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS # ########################################################### closest.t01...ok closest.t02...ok closest.t03...ok closest.t04...ok closest.t05...ok closest.t06...ok closest.t07...ok closest.t08...ok closest.t09...ok closest.t10...ok closest.t11...ok closest.t12...ok closest.t13...ok closest.t14...ok closest.t15...ok closest.t16...ok closest.t17...ok closest.t18...ok closest.t19...ok closest.20...ok closest.21...ok closest.22...ok closest.23...ok ########################################################### # # K CLOSEST HITS TESTS # ########################################################### kclosest.t1...ok kclosest.t2...ok kclosest.t3...ok kclosest.t4...ok kclosest.t5...ok kclosest.t6...ok kclosest.t7...ok kclosest.t8...ok kclosest.t9...ok kclosest.t10...ok kclosest.t11...Warning: Fewer hits (5) found on chr1 than requested (7). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t12...Warning: Fewer hits (5) found on chr1 than requested (7). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t13...Warning: Fewer hits (3) found on chr1 than requested (7). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t14...Warning: Fewer hits (1) found on chr1 than requested (7). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t15...Warning: Fewer hits (11) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t16...ok kclosest.t17...Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t18...Warning: Fewer hits (11) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t19...Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t20...Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t21...Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t22...Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t23...Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t24...Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t25...Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t26...Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t27...Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t28...Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t29...Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t30...ok kclosest.t31...Warning: Fewer hits (9) found on chr1 than requested (10). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t32...Warning: Fewer hits (9) found on chr1 than requested (10). It is likely that there are fewer total records on that chromosome than requested. ok kclosest.t33...ok kclosest.t34...ok kclosest.t35...ok kclosest.t36...ok kclosest.t37...ok kclosest.t38...ok kclosest.t39...ok kclosest.t40...ok kclosest.t41...ok kclosest.t42...ok kclosest.t43...ok kclosest.t44...ok kclosest.t45...ok Testing bedtools cluster: cluster.t1...ok cluster.t2...ok Testing bedtools complement: complement.t1...ok complement.t2...ok complement.t3...ok complement.t4...ok complement.t5...ok complement.t6...ok complement.t7...ok complement.t8...ok complement.t9...ok complement.t9...ok complement.t10...ok Testing bedtools coverage: coverage.t1...ok coverage.t1b...ok coverage.t2...ok coverage.t2b...ok coverage.t3...ok coverage.t3b...ok coverage.t4...ok coverage.t4b...ok coverage.t5...ok coverage.t5b...ok coverage.t6...ok coverage.t6b...ok coverage.t7...ok coverage.t7b...ok coverage.t8...ok coverage.t8b...ok coverage.t9...ok coverage.t9b...ok coverage.t10...ok coverage.t10b...ok coverage.t11...ok coverage.t11b...ok coverage.t12...ok coverage.t12b...ok coverage.t13...ok coverage.t13b...ok coverage.t14...ok coverage.t14b...ok coverage.t15...ok coverage.t15b...ok coverage.t16...ok coverage.t16b...ok coverage.t17...ok coverage.t17b...ok coverage.t18...ok coverage.t18b...ok coverage.t19...ok coverage.t19b...ok coverage.t20...ok Testing bedtools expand: expand.t1...ok expand.t2...ok expand.t3...ok Testing bedtools fisher: fisher.t1...ok fisher.t2...ok fisher.t3...ok fisher.t4...ok fisher.t5...ok fisher.t6...ok Testing bedtools flank: flank.t1...ok flank.t2...ok flank.t3...ok flank.t4...ok flank.t5...ok flank.t6...ok flank.t7...ok flank.t8...ok flank.t9...ok flank.t10...ok flank.t11...ok Testing bedtools general: general.t01...ok general.t02...ok general.t03...ok general.t05...ok general.t06...ok general.t07...ok general.t08...ok general.t09...ok general.t10...ok general.t11...ok general.t12...ok general.t13...ok general.t14...ok general.15...ok general.t16...ok general.t17...ok general.t18...ok general.t19...ok general.t20...ok general.t21...ok general.22...ok general.t23...ok general.t24...ok general.t25...ok general.t26...ok general.t27...ok general.t28...ok general.29...ok general.t30...ok general.t31...ok general.t32...ok general.t33...ok general.t34...ok general.t35...ok general.36...ok general.t37...ok general.t38...ok general.t39...ok general.t40...ok general.t41...ok general.t42...ok general.t43...ok general.t44...ok general.t45...ok general.t46...ok Testing bedtools genomecov: genomecov.t1...ok genomecov.t2...ok genomecov.t3...ok genomecov.t4...ok genomecov.t5...ok genomecov.t6...ok genomecov.t7...ok genomecov.t8...ok genomecov.t9...ok genomecov.t10...ok genomecov.t11...ok genomecov.t12...ok genomecov.t13...ok genomecov.t14...ok genomecov.t15...ok genomecov.t16...ok genomecov.t17...ok genomecov.t18...ok Testing bedtools getfasta: getfasta.t01...ok getfasta.t02...ok getfasta.t03...ok getfasta.t04...ok getfasta.t05...ok getfasta.t06...ok getfasta.t07...ok getfasta.t08...ok getfasta.t09...ok getfasta.t10...ok getfasta.t11...ok getfasta.t12a...ok getfasta.t12a...ok getfasta.t12b...ok getfasta.t13a...ok getfasta.t13b...ok getfasta.t13c...ok getfasta.t14...ok getfasta.t15...ok getfasta.t134..ok getfasta.t16..ok getfasta.t17..ok getfasta.t18...ok Testing bedtools groupby: groupby.t1...ok groupby.t2...ok groupby.t3...ok groupby.t4...ok groupby.t5...ok groupby.t6...ok groupby.t7...ok groupby.t8...ok groupby.t9...ok groupby.t10...ok groupby.t11...ok groupby.t12...ok groupby.t13...ok groupby.t14...ok groupby.t16...ok groupby.t17...ok groupby.t18...ok groupby.t19...\c ok groupby.t20...\c ok Testing bedtools intersect: intersect.t01...ok intersect.t02...ok intersect.t03...ok intersect.t04...ok intersect.t05...ok intersect.t06...ok intersect.t07...ok intersect.t08...ok intersect.t09...ok intersect.t10...ok intersect.t11...ok intersect.t12...ok intersect.t13...ok intersect.t14...ok intersect.t15...ok intersect.t16...ok intersect.t17...ok intersect.t18...ok intersect.t19...ok intersect.t20...ok intersect.t21...ok intersect.t22...ok intersect.t22.a...ok intersect.t22.b...ok intersect.t22.c...ok intersect.t22.d...ok intersect.t22.e...ok intersect.t22.f...ok intersect.t22.g...ok intersect.t22.h...ok intersect.t22.i...ok intersect.t22.j...ok intersect.t22.j...ok intersect.t22.k...ok intersect.t22.l...ok intersect.t22.m...ok intersect.t22.n...ok intersect.t22.o...ok intersect.t22.p...ok intersect.t22.q...ok intersect.t22.r...ok intersect.t22.s...ok intersect.t22.t...ok intersect.t22.u...ok intersect.t22.v...ok intersect.t22.w...ok intersect.t23...ok intersect.t24...ok intersect.t25...ok intersect.t26...ok intersect.t27...ok intersect.t28...ok intersect.t29...ok intersect.t30...ok intersect.t31...ok intersect.t32...ok intersect.t33...ok intersect.t34...ok intersect.t35...ok intersect.t36...ok intersect.t37...ok intersect.t38...ok intersect.t39...ok intersect.t40...ok intersect.t41...ok intersect.t42...ok intersect.t43...ok intersect.t44...ok intersect.t45...ok intersect.t46...ok intersect.t47...ok intersect.t48...ok intersect.t49...ok intersect.t50...ok intersect.t51...ok intersect.t52...ok intersect.t53...ok intersect.t54...ok intersect.t55...ok intersect.t56...ok intersect.t57...ok intersect.t58...ok intersect.t59...ok intersect.t60...ok intersect.t61...ok intersect.t62...ok intersect.t63...ok intersect.t64...ok intersect.t65...ok intersect.t66...ok intersect.t67...ok intersect.t68...ok intersect.t69...ok intersect.t70...ok intersect.t71...ok intersect.t72...ok intersect.t73...ok intersect.t74...ok intersect.t75...ok intersect.t76...ok intersect.t77...ok intersect.t78...ok intersect.t79...ok intersect.t80...ok intersect.t81...ok intersect.t82...ok intersect.t83...ok intersect.new.t01...ok intersect.new.t02...ok intersect.new.t03...ok intersect.new.t04...ok intersect.new.t05...ok intersect.new.t06...ok intersect.new.t07...ok intersect.new.t08...ok intersect.new.t09...ok intersect.new.t10...ok intersect.new.t11...ok intersect.new.t12...ok intersect.new.t13...ok intersect.new.t14...ok intersect.new.t15...ok intersect.new.t16...ok intersect.new.t17...ok intersect.new.t18...ok intersect.new.t19...ok intersect.new.t20...ok intersect.new.t20.b...ok intersect.new.t20.c...ok intersect.new.t21...ok intersect.new.t22...ok intersect.new.t23...ok intersect.new.t24...ok intersect.new.t25...ok intersect.new.t26...ok intersect.new.t27...ok intersect.new.t28...ok intersect.new.t29...ok intersect.new.t30...ok intersect.new.t31...ok intersect.new.t32...ok intersect.new.t33...ok intersect.new.t34...ok intersect.new.t35...ok intersect.new.t36...ok intersect.new.t37...ok intersect.new.t38...ok intersect.new.t39...ok intersect.new.t40...ok intersect.new.t41...ok intersect.new.t42...ok intersect.new.t43...ok intersect.new.t44...ok intersect.new.t45...ok intersect.new.t46...ok intersect.new.t47...ok intersect.new.t48...ok intersect.new.t49...ok intersect.new.t50...ok intersect.new.t51...ok intersect.new.t52...ok intersect.new.t53...ok intersect.new.t54...ok intersect.new.t55...ok intersect.new.t56...ok intersect.new.t57...ok intersect.new.t58...ok intersect.new.t59...ok intersect.new.t60...ok intersect.new.t61...ok intersect.new.t62...ok intersect.new.t63...ok intersect.new.t64...ok intersect.new.t65...ok intersect.new.t66...ok intersect.new.t67a...ok intersect.new.t67b...ok intersect.new.t68a...ok intersect.new.t68b...ok intersect.new.t69...ok intersect.new.t70...ok intersect.new.t71...ok intersect.new.t72...ok intersect.new.t73...ok intersect.new.t74...ok intersect.new.t75...ok intersect.new.t76...ok intersect.new.t77...ok intersect.new.t78...ok intersect.new.t79...ok intersect.new.t80...ok intersect.new.t81...ok ########################################################### # # MULTIPLE DATABASE INTERSECTION # ########################################################### intersect.t01...ok intersect.t02...ok intersect.t03...ok intersect.t04...ok intersect.t05...ok intersect.t06...ok intersect.t07...ok intersect.t08...ok intersect.t09...ok intersect.t10...ok intersect.t11...ok intersect.t12...ok intersect.t13...ok intersect.t14...ok intersect.t15...ok intersect.t16...ok intersect.t17...ok intersect.t18...ok intersect.t13...ok intersect.t19...ok intersect.t20...ok intersect.t21...ok intersect.t22...ok intersect.t23...ok intersect.t24...ok ########################################################### # # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS # ########################################################### intersect.t01...ok intersect.t02...ok intersect.t03...ok intersect.t04...ok intersect.t05...ok intersect.t06...ok intersect.t07...ok intersect.t08...ok intersect.t09...ok intersect.t10...ok intersect.t11...ok intersect.t12...ok intersect.t13...ok intersect.t14...ok intersect.t15...ok intersect.t16...ok intersect.t17...ok intersect.t18...ok intersect.t19...ok intersect.20...ok intersect.21...ok intersect.22...ok intersect.23...ok Testing bedtools jaccard: jaccard.t01...ok jaccard.t02...ok jaccard.t03...ok jaccard.t05...ok jaccard.t06...ok jaccard.t07...ok jaccard.t08...ok jaccard.t09...ok jaccard.t10...ok jaccard.t11...ok jaccard.t12...ok jaccard.t13...ok jaccard.t14...ok jaccard.t15...ok jaccard.t16...ok Testing bedtools makewindows: makewindows.t01...ok makewindows.t02...ok makewindows.t03...ok makewindows.t04...ok makewindows.t05...ok makewindows.t06...ok makewindows.t07...ok makewindows.t08...ok makewindows.t09...ok Testing bedtools map: map.t01...ok map.t02...ok map.t03...ok map.t04...ok map.t05...ok map.t06...ok map.t07...ok map.t08...ok map.t09...ok map.t10...ok map.t11...ok map.t12...ok map.t13...ok map.t14...ok map.t15...ok map.t16...ok map.t17...ok map.t18...ok map.t19...ok map.t20...ok map.t21...ok map.t22..ok map.t23..ok map.t24..ok map.t25..ok map.t26..ok map.t27..ok map.t28..ok map.t29..ok map.t30..ok map.t31..ok map.t32..ok map.t33..ok map.t33..ok map.t33..ok map.t34..ok map.t35..ok map.t36..ok map.t37..ok map.t38..ok map.t39..ok map.t40..ok map.t41..ok map.t42..ok map.t43..ok map.t44...ok map.t45...ok map.t46...ok map.t47...ok map.t48...ok map.t49...ok map.t50...ok map.t51...ok map.t52...ok map.t53...ok map.t54...ok map.t55...ok Testing bedtools merge: merge.t1...ok merge.t2...ok merge.t3...ok merge.t4...ok merge.t5...ok merge.t6...ok merge.t7...ok merge.t8...ok merge.t9a...ok merge.t9b...ok merge.t10...ok merge.t11...ok merge.t12...ok merge.t13...ok merge.t14...ok merge.t15...ok merge.t16...ok merge.t17...ok merge.t18...ok merge.t19...ok merge.t20...ok merge.t21...ok merge.t22...ok merge.t23a...ok merge.t23b...ok merge.t24...ok merge.t25...ok merge.t26...ok merge.t27...ok merge.t28...ok merge.t29...ok merge.t30...ok merge.t31...ok merge.t32...ok merge.t33...ok merge.t34...ok merge.t35...ok merge.t36...ok merge.t37...ok merge.t38...ok merge.t39...ok merge.t40...ok merge.t41...ok merge.t42...ok merge.t43...ok merge.t44a...ok merge.t44b...skipped - could not find vcfSVtest.2.vcf merge.t45...ok merge.t46...ok merge.t47...ok merge.t48...ok merge.t49...ok merge.t50...ok Testing bedtools multicov: multicov.t1...ok multicov.t2...ok multicov.t3...ok multicov.t4...ok multicov.t5...ok multicov.t6...ok multicov.t7...ok multicov.t8...ok multicov.t9...ok multicov.t10...ok Testing bedtools negativecontrol: Testing bedtools reldist: reldist.t01...ok reldist.t02...ok reldist.t03...ok reldist.t02...ok Testing bedtools sample: sample.t01...ok sample.new.t02...ok sample.new.t03...ok sample.new.t04...ok sample.new.t05...ok sample.new.t06...ok sample.new.t07...ok sample.new.t08...ok sample.new.t09...ok Testing bedtools shift: shift.t1...ok shift.t2...ok shift.t3...ok shift.t3...ok shift.t4...ok shift.t5...ok shift.t6...ok shift.t7...ok shift.t8...ok shift.t9...ok shift.t10...ok shift.t11...ok Testing bedtools shuffle: shuffle.t1...ok shuffle.t2...ok shuffle.t3...ok shuffle.t4...ok shuffle.t5...ok shuffle.t6...ok Testing bedtools slop: slop.t1...ok slop.t2...ok slop.t3...ok slop.t4...ok slop.t5...ok slop.t6...ok slop.t7...ok slop.t8...ok slop.t9...ok slop.t10...ok slop.t11...ok slop.t12...ok slop.t13...ok slop.t14...ok slop.t15...ok slop.t16...ok slop.t17...ok slop.t18...ok slop.t19...ok slop.t20...ok slop.t21...ok slop.t22...ok Testing bedtools sort: sort.t01...ok sort.t02...ok sort.t03...ok sort.t04...ok sort.t05...ok sort.t06...ok sort.t07...ok sort.t08...ok sort.t09...ok sort.t10...ok Testing bedtools spacing: spacing.t01...ok Testing bedtools split: split.01.size...ok split.02.simple...ok spliit.03.simple...ok Testing bedtools subtract: subtract.t1...ok subtract.t2...ok subtract.t3...ok subtract.t4...ok subtract.t5...ok subtract.t6...ok subtract.t7...ok subtract.t8...ok subtract.t9...ok subtract.t10...ok subtract.t11...ok subtract.t12...ok subtract.t13...ok subtract.t14...ok subtract.t15...ok subtract.t16...ok subtract.t17...ok subtract.t18...ok subtract.t19...ok subtract.t20...ok subtract.t21...ok -------------------------- Test Results -------------------------- Tools passing: bamtobed bamtofastq bed12tobed6 bedtobam bigchroms closest cluster complement coverage expand fisher flank general genomecov getfasta groupby intersect jaccard makewindows map merge multicov reldist sample shift shuffle slop sort spacing split subtract Tools failing: negativecontrol 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/reproducible-path/bedtools-2.31.1+dfsg' rm -fr -- /tmp/dh-xdg-rundir-VHzIxBQ2 make[1]: Leaving directory '/build/reproducible-path/bedtools-2.31.1+dfsg' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/bedtools.substvars debian/bedtools-test.substvars rm -fr -- debian/.debhelper/generated/bedtools/ debian/bedtools/ debian/tmp/ debian/.debhelper/generated/bedtools-test/ debian/bedtools-test/ rm -f debian/bedtools-test.debhelper.log debian/bedtools.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/bedtools-2.31.1+dfsg' dh_auto_install -- VERBOSE=1 install -m0755 -d /build/reproducible-path/bedtools-2.31.1\+dfsg/debian/tmp make -j42 install DESTDIR=/build/reproducible-path/bedtools-2.31.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/bedtools-2.31.1+dfsg' mkdir -p /build/reproducible-path/bedtools-2.31.1+dfsg/debian/tmp/usr/local/bin for file in bin/* ; do \ cp -f $file /build/reproducible-path/bedtools-2.31.1+dfsg/debian/tmp/usr/local/bin; \ done make[2]: Leaving directory '/build/reproducible-path/bedtools-2.31.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/bedtools-2.31.1+dfsg' rm -f debian/bedtools-test.debhelper.log debian/bedtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/bedtools-2.31.1+dfsg' dh_install install -m0755 -d debian/bedtools/usr/bin cp --reflink=auto -a debian/tmp/usr/local/bin/annotateBed debian/tmp/usr/local/bin/bamToBed debian/tmp/usr/local/bin/bamToFastq debian/tmp/usr/local/bin/bed12ToBed6 debian/tmp/usr/local/bin/bedToBam debian/tmp/usr/local/bin/bedToIgv debian/tmp/usr/local/bin/bedpeToBam debian/tmp/usr/local/bin/bedtools debian/tmp/usr/local/bin/closestBed debian/tmp/usr/local/bin/clusterBed debian/tmp/usr/local/bin/complementBed debian/tmp/usr/local/bin/coverageBed debian/tmp/usr/local/bin/expandCols debian/tmp/usr/local/bin/fastaFromBed debian/tmp/usr/local/bin/flankBed debian/tmp/usr/local/bin/genomeCoverageBed debian/tmp/usr/local/bin/getOverlap debian/tmp/usr/local/bin/groupBy debian/tmp/usr/local/bin/intersectBed debian/tmp/usr/local/bin/linksBed debian/tmp/usr/local/bin/mapBed debian/tmp/usr/local/bin/maskFastaFromBed debian/tmp/usr/local/bin/mergeBed debian/tmp/usr/local/bin/multiBamCov debian/tmp/usr/local/bin/multiIntersectBed debian/tmp/usr/local/bin/nucBed debian/tmp/usr/local/bin/pairToBed debian/tmp/usr/local/bin/pairToPair debian/tmp/usr/local/bin/randomBed debian/tmp/usr/local/bin/shiftBed debian/tmp/usr/local/bin/shuffleBed debian/tmp/usr/local/bin/slopBed debian/tmp/usr/local/bin/sortBed debian/tmp/usr/local/bin/subtractBed debian/tmp/usr/local/bin/tagBam debian/tmp/usr/local/bin/unionBedGraphs debian/tmp/usr/local/bin/windowBed debian/tmp/usr/local/bin/windowMaker debian/bedtools/usr/bin/ install -m0755 -d debian/bedtools/usr/share/bash-completion/completions cp --reflink=auto -a ./debian/bash_completion/bedtools debian/bedtools/usr/share/bash-completion/completions/ install -m0755 -d debian/bedtools/usr/share/bedtools cp --reflink=auto -a ./genomes debian/bedtools/usr/share/bedtools/ install -m0755 -d debian/bedtools-test/usr/share/bedtools/test cp --reflink=auto -a ./test/intersect debian/bedtools-test/usr/share/bedtools/test/ install -m0755 -d debian/bedtools-test/usr/share/bedtools/test cp --reflink=auto -a ./debian/test_missing_files/intersect debian/bedtools-test/usr/share/bedtools/test/ install -m0755 -d debian/bedtools-test/usr/share/bedtools/data cp --reflink=auto -a ./data/aluY.chr1.bed.gz ./data/gerp.chr1.bed.gz ./data/knownGene.hg18.chr21.bed ./data/knownGene.hg18.chr21.short.bed ./data/refseq.chr1.exons.bed.gz ./data/simpleRepeats.chr1.bed.gz debian/bedtools-test/usr/share/bedtools/data/ install -m0755 -d debian/bedtools-test/usr/share/bedtools/test cp --reflink=auto -a ./test/bamtobed ./test/bamtofastq ./test/bed12tobed6 ./test/bedtobam ./test/bigchroms ./test/closest ./test/cluster ./test/complement ./test/coverage ./test/expand ./test/fisher ./test/flank ./test/general ./test/genomecov ./test/getfasta ./test/groupby ./test/jaccard ./test/makewindows ./test/map ./test/merge ./test/multicov ./test/negativecontrol ./test/reldist ./test/sample ./test/shift ./test/shuffle ./test/slop ./test/sort ./test/spacing ./test/split ./test/subtract ./test/test.sh debian/bedtools-test/usr/share/bedtools/test/ # make sure all *.sh files are featuring a '#!/bin/bash' as first line # since there are at least two files (test/intersect/{new_test-intersect.sh,performanceTest.sh} # requiring bash this is taken for all scripts instead of checking first via /bin/sh -n for sh in `find /build/reproducible-path/bedtools-2.31.1+dfsg/debian -name "*.sh"` ; do \ if ! head -n1 ${sh} | grep -q '^#! */bin/[ba]*sh' ; then \ sed -i '1 i #!/bin/bash' ${sh} ; \ fi ; \ done make[1]: Leaving directory '/build/reproducible-path/bedtools-2.31.1+dfsg' dh_installdocs install -m0755 -d debian/bedtools/usr/share/doc/bedtools install -m0755 -d debian/bedtools/usr/share/doc/bedtools cp --reflink=auto -a ./README.md debian/bedtools/usr/share/doc/bedtools cp --reflink=auto -a ./debian/README.test debian/bedtools/usr/share/doc/bedtools cp --reflink=auto -a ./debian/tests/run-unit-test debian/bedtools/usr/share/doc/bedtools chmod -R u\+rw,go=rX debian/bedtools/usr/share/doc install -p -m0644 debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright install -m0755 -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 -m0755 -d debian/bedtools-test/usr/share/doc/bedtools-test install -p -m0644 debian/.debhelper/generated/bedtools-test/dh_installchangelogs.dch.trimmed debian/bedtools-test/usr/share/doc/bedtools-test/changelog.Debian install -m0755 -d debian/bedtools/usr/share/doc/bedtools install -p -m0644 debian/.debhelper/generated/bedtools/dh_installchangelogs.dch.trimmed debian/bedtools/usr/share/doc/bedtools/changelog.Debian dh_perl dh_link dh_strip_nondeterminism Using 1701717191 as canonical time 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/test/general/non-empty.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/test/merge/chained.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/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/data/simpleRepeats.chr1.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/data/gerp.chr1.bed.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 gzip -9nf usr/share/doc/bedtools/changelog.Debian cd '/build/reproducible-path/bedtools-2.31.1+dfsg' cd '/build/reproducible-path/bedtools-2.31.1+dfsg' rm -f debian/bedtools-test.debhelper.log debian/bedtools.debhelper.log debian/rules override_dh_fixperms-arch make[1]: Entering directory '/build/reproducible-path/bedtools-2.31.1+dfsg' dh_fixperms find debian/bedtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/bedtools/usr/share/doc -type f -a -true -a ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/bedtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/bedtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/bedtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x chmod -x /build/reproducible-path/bedtools-2.31.1+dfsg/debian/bedtools/usr/share/bedtools/genomes/*.genome find /build/reproducible-path/bedtools-2.31.1+dfsg/debian -name "*.bed" -executable -exec chmod -x \{\} \; find /build/reproducible-path/bedtools-2.31.1+dfsg/debian -name "*.sam" -executable -exec chmod -x \{\} \; find /build/reproducible-path/bedtools-2.31.1+dfsg/debian -name "*.sh" -not -executable -exec chmod +x \{\} \; make[1]: Leaving directory '/build/reproducible-path/bedtools-2.31.1+dfsg' dh_fixperms -Nbedtools find debian/bedtools-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/bedtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/bedtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/bedtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/bedtools-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing dh_dwz -a dwz -- debian/bedtools/usr/bin/bedtools dh_strip -a install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/1a objcopy --only-keep-debug --compress-debug-sections debian/bedtools/usr/bin/bedtools debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/1a/2766354a3e5ea8cbf84dc7fe74d99bdd5e3666.debug chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/1a/2766354a3e5ea8cbf84dc7fe74d99bdd5e3666.debug strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools objcopy --add-gnu-debuglink debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/1a/2766354a3e5ea8cbf84dc7fe74d99bdd5e3666.debug debian/bedtools/usr/bin/bedtools install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/usr/share/doc ln -s bedtools debian/.debhelper/bedtools/dbgsym-root/usr/share/doc/bedtools-dbgsym install -m0755 -d debian/.debhelper/bedtools dh_makeshlibs -a rm -f debian/bedtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/bedtools/DEBIAN dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools dh_installdeb install -m0755 -d debian/bedtools/DEBIAN install -m0755 -d debian/bedtools-test/DEBIAN dh_gencontrol install -m0755 -d debian/bedtools/DEBIAN echo misc:Depends= >> debian/bedtools.substvars echo misc:Pre-Depends= >> debian/bedtools.substvars install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/DEBIAN dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -cdebian/control -Pdebian/.debhelper/bedtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=bedtools-dbgsym "-DDepends=bedtools (= \${binary:Version})" "-DDescription=debug symbols for bedtools" -DBuild-Ids=1a2766354a3e5ea8cbf84dc7fe74d99bdd5e3666 -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/bedtools-test/DEBIAN echo misc:Depends= >> debian/bedtools-test.substvars echo misc:Pre-Depends= >> debian/bedtools-test.substvars dpkg-gencontrol -pbedtools-test -ldebian/changelog -Tdebian/bedtools-test.substvars -cdebian/control -Pdebian/bedtools-test chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -cdebian/control -Pdebian/bedtools chmod 0644 -- debian/bedtools-test/DEBIAN/control chmod 0644 -- debian/bedtools/DEBIAN/control dh_md5sums install -m0755 -d debian/bedtools/DEBIAN install -m0755 -d debian/bedtools-test/DEBIAN cd debian/bedtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/bedtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/bedtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/bedtools/dbgsym-root/DEBIAN cd debian/.debhelper/bedtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums 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: building package 'bedtools' in '../bedtools_2.31.1+dfsg-2_amd64.deb'. dpkg-deb: building package 'bedtools-dbgsym' in '../bedtools-dbgsym_2.31.1+dfsg-2_amd64.deb'. dpkg-deb: building package 'bedtools-test' in '../bedtools-test_2.31.1+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary -O../bedtools_2.31.1+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../bedtools_2.31.1+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from bedtools-2.31.1+dfsg/debian/source/options: --single-debian-patch dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2932485/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2932485/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/2932485 and its subdirectories I: Current time: Thu Jan 15 13:39:55 +14 2026 I: pbuilder-time-stamp: 1768433995