I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 16 04:05:30 +14 2021 I: pbuilder-time-stamp: 1629036330 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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_2.27.1+dfsg-4.dsc] I: copying [./bedtools_2.27.1+dfsg.orig.tar.xz] I: copying [./bedtools_2.27.1+dfsg-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Feb 15 03:14:15 2019 +14 gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bedtools_2.27.1+dfsg-4.dsc dpkg-source: info: extracting bedtools in bedtools-2.27.1+dfsg dpkg-source: info: unpacking bedtools_2.27.1+dfsg.orig.tar.xz dpkg-source: info: unpacking bedtools_2.27.1+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gzstream.h.patch dpkg-source: info: applying fix_test_script.patch dpkg-source: info: applying remove_barski_binding_site.png.patch dpkg-source: info: applying reproducible_build.patch dpkg-source: info: applying louder dpkg-source: info: applying flag_no_overwrite I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/29987/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/29987/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/29987/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=63e8635f077241859cf37006a1140815 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=29987 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/tmp.YnyuH5dRJ9/pbuilderrc_9EGM --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.YnyuH5dRJ9/b2 --logfile b2/build.log bedtools_2.27.1+dfsg-4.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://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Aug 16 04:05 sh -> bash lrwxrwxrwx 1 root root 4 Aug 7 22:24 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/29987/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 (>= 11~), python, zlib1g-dev, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on python; however: Package python is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools 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} bsdmainutils{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} libbsd0{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhts2{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} samtools{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl cwltool krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 28.0 MB of archives. After unpacking 98.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u6 [1539 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-11 [305 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 samtools amd64 1.9-4 [443 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Fetched 28.0 MB in 1s (48.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. 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Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u1) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up libhts2:amd64 (1.9-11) ... Setting up po-debconf (1.0.21) ... Setting up samtools (1.9-4) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up debhelper (12.1.1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/bedtools-2.27.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package bedtools dpkg-buildpackage: info: source version 2.27.1+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Charles Plessy dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from bedtools-2.27.1+dfsg/debian/source/options: --single-debian-patch fakeroot debian/rules clean dh clean dh_auto_clean make -j15 clean make[1]: Entering directory '/build/bedtools-2.27.1+dfsg' * Cleaning-up BamTools API * Cleaning up. make[1]: Leaving directory '/build/bedtools-2.27.1+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 \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j15 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bedtools-2.27.1+dfsg' $CXXFLAGS is [-g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11] Building BEDTools: ========================================================= * Creating BamTools API DETECTED_VERSION = v2.27.1 CURRENT_VERSION = Updating version file. - Building in src/utils/FileRecordTools/FileReaders - Building in src/utils/FileRecordTools - Building in src/utils/FileRecordTools/Records - Building in src/utils/bedFile - Building in src/utils/BinTree * compiling FileReader.cpp * compiling SingleLineDelimTextFileReader.cpp - Building in src/utils/version g++ -c -o ../../../../obj//FileReader.o FileReader.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//BamTools/include/ -I../../../utils//BamTools/src/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//general/ -I../../../utils//gzstream/ -I../../../utils//version/ -I../../../utils//lineFileUtilities/ * compiling FileRecordMgr.cpp - Building in src/utils/bedGraphFile * compiling Record.cpp * compiling FileRecordMgr.cpp * compiling BamFileReader.cpp g++ -c -o ../../../../obj//Record.o Record.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ - Building in FileReaders g++ -c -o ../../../obj//FileRecordMgr.o FileRecordMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//fileType/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//GenomeFile/ -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ g++ -c -o ../../../../obj//SingleLineDelimTextFileReader.o SingleLineDelimTextFileReader.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//BamTools/include/ -I../../../utils//BamTools/src/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//general/ -I../../../utils//gzstream/ -I../../../utils//version/ -I../../../utils//lineFileUtilities/ * compiling EmptyRecord.cpp * compiling bedFile.cpp g++ -c -o ../../../obj//FileRecordMgr.o FileRecordMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//fileType/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//GenomeFile/ -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ g++ -c -o ../../../../obj//BamFileReader.o BamFileReader.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//BamTools/include/ -I../../../utils//BamTools/src/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//general/ -I../../../utils//gzstream/ -I../../../utils//version/ -I../../../utils//lineFileUtilities/ * compiling BinTree.cpp g++ -c -o ../../../../obj//EmptyRecord.o EmptyRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ g++ -c -o ../../../obj//bedFile.o bedFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//gzstream/ -I../../utils//fileType/ -I../../utils//stringUtilities/ g++ -c -o ../../../obj//BinTree.o BinTree.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//Contexts/ -I../../utils//GenomeFile/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling Bed3Interval.cpp * compiling bedGraphFile.cpp g++ -c -o ../../../obj//bedGraphFile.o bedGraphFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//gzstream/ -I../../utils//fileType/ - Building in src/utils/chromsweep * compiling BufferedStreamMgr.cpp g++ -c -o ../../../../obj//BufferedStreamMgr.o BufferedStreamMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//BamTools/include/ -I../../../utils//BamTools/src/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//general/ -I../../../utils//gzstream/ -I../../../utils//version/ -I../../../utils//lineFileUtilities/ g++ -c -o ../../../../obj//Bed3Interval.o Bed3Interval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling version.cpp g++ -c -o ../../../obj//version.o version.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 * compiling FileReader.cpp g++ -c -o ../../../../obj//FileReader.o FileReader.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//BamTools/include/ -I../../../utils//BamTools/src/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//general/ -I../../../utils//gzstream/ -I../../../utils//version/ -I../../../utils//lineFileUtilities/ * compiling chromsweep.cpp g++ -c -o ../../../obj//chromsweep.o chromsweep.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//bedFile/ -I../../utils//gzstream/ -I../../utils//fileType/ - Building in src/utils/Contexts * compiling ContextBase.cpp g++ -c -o ../../../obj//ContextBase.o ContextBase.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling InputStreamMgr.cpp g++ -c -o ../../../../obj//InputStreamMgr.o InputStreamMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//BamTools/include/ -I../../../utils//BamTools/src/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//general/ -I../../../utils//gzstream/ -I../../../utils//version/ -I../../../utils//lineFileUtilities/ * compiling Bed4Interval.cpp g++ -c -o ../../../../obj//Bed4Interval.o Bed4Interval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling BedGraphInterval.cpp g++ -c -o ../../../../obj//BedGraphInterval.o BedGraphInterval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling ContextIntersect.cpp g++ -c -o ../../../obj//ContextIntersect.o ContextIntersect.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling SingleLineDelimTextFileReader.cpp g++ -c -o ../../../../obj//SingleLineDelimTextFileReader.o SingleLineDelimTextFileReader.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//BamTools/include/ -I../../../utils//BamTools/src/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//general/ -I../../../utils//gzstream/ -I../../../utils//version/ -I../../../utils//lineFileUtilities/ * compiling FileRecordMergeMgr.cpp g++ -c -o ../../../obj//FileRecordMergeMgr.o FileRecordMergeMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//fileType/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//GenomeFile/ -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling FileRecordMergeMgr.cpp g++ -c -o ../../../obj//FileRecordMergeMgr.o FileRecordMergeMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//fileType/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//GenomeFile/ -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ - Building in src/utils/general * compiling ParseTools.cpp g++ -c -o ../../../obj//ParseTools.o ParseTools.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//version/ * compiling Bed5Interval.cpp g++ -c -o ../../../../obj//Bed5Interval.o Bed5Interval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling PushBackStreamBuf.cpp g++ -c -o ../../../obj//PushBackStreamBuf.o PushBackStreamBuf.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//version/ - Building in src/utils/gzstream g++ -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ../../../obj//gzstream.o gzstream.C -I. * compiling Bed6Interval.cpp g++ -c -o ../../../../obj//Bed6Interval.o Bed6Interval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ - Building in src/utils/fileType * compiling fileType.cpp g++ -c -o ../../../obj//fileType.o fileType.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//BamTools/include/ -I../../utils//general * compiling PlusFields.cpp g++ -c -o ../../../../obj//PlusFields.o PlusFields.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling BedPlusInterval.cpp g++ -c -o ../../../../obj//BedPlusInterval.o BedPlusInterval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling CompressionTools.cpp g++ -c -o ../../../obj//CompressionTools.o CompressionTools.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//version/ * compiling Tokenizer.cpp g++ -c -o ../../../obj//Tokenizer.o Tokenizer.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//version/ * compiling FileRecordTypeChecker.cpp g++ -c -o ../../../obj//FileRecordTypeChecker.o FileRecordTypeChecker.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//BamTools/include/ -I../../utils//general - Building in Records * compiling Bed5Interval.cpp g++ -c -o ../../../../obj//Bed5Interval.o Bed5Interval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ - Building in src/utils/bedFilePE * compiling bedFilePE.cpp g++ -c -o ../../../obj//bedFilePE.o bedFilePE.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//bedFile/ -I../../utils//gzstream/ -I../../utils//fileType/ * compiling ContextFisher.cpp g++ -c -o ../../../obj//ContextFisher.o ContextFisher.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling Bed12Interval.cpp g++ -c -o ../../../../obj//Bed12Interval.o Bed12Interval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling CommonHelp.cpp * compiling ContextMap.cpp g++ -c -o ../../../obj//CommonHelp.o CommonHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//version/ g++ -c -o ../../../obj//ContextMap.o ContextMap.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling InputStreamMgr.cpp g++ -c -o ../../../../obj//InputStreamMgr.o InputStreamMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//BamTools/include/ -I../../../utils//BamTools/src/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//general/ -I../../../utils//gzstream/ -I../../../utils//version/ -I../../../utils//lineFileUtilities/ * compiling BamRecord.cpp g++ -c -o ../../../../obj//BamRecord.o BamRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling GffRecord.cpp g++ -c -o ../../../../obj//GffRecord.o GffRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ FileRecordTypeChecker.cpp: In member function 'bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)': FileRecordTypeChecker.cpp:365:19: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for (int j=0; j < len; j++) { ~~^~~~~ * compiling GffPlusRecord.cpp g++ -c -o ../../../../obj//GffPlusRecord.o GffPlusRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ - Building in src/utils/KeyListOps * compiling KeyListOps.cpp g++ -c -o ../../../obj//KeyListOps.o KeyListOps.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//GenomeFile/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling Bed6Interval.cpp g++ -c -o ../../../../obj//Bed6Interval.o Bed6Interval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling ContextSample.cpp g++ -c -o ../../../obj//ContextSample.o ContextSample.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling VcfRecord.cpp g++ -c -o ../../../../obj//VcfRecord.o VcfRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling NoPosPlusRecord.cpp g++ -c -o ../../../../obj//NoPosPlusRecord.o NoPosPlusRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ - Building in src/utils/NewChromsweep * compiling ContextSpacing.cpp g++ -c -o ../../../obj//ContextSpacing.o ContextSpacing.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling BlockMgr.cpp g++ -c -o ../../../../obj//BlockMgr.o BlockMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling NewChromsweep.cpp g++ -c -o ../../../obj//NewChromsweep.o NewChromsweep.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//Contexts/ -I../../utils//GenomeFile/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling StrandQueue.cpp g++ -c -o ../../../../obj//StrandQueue.o StrandQueue.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling Bed12Interval.cpp g++ -c -o ../../../../obj//Bed12Interval.o Bed12Interval.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling RecordMgr.cpp g++ -c -o ../../../../obj//RecordMgr.o RecordMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ - Building in src/utils/sequenceUtilities * compiling sequenceUtils.cpp g++ -c -o ../../../obj//sequenceUtils.o sequenceUtils.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 * compiling ContextMerge.cpp g++ -c -o ../../../obj//ContextMerge.o ContextMerge.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling RecordList.cpp g++ -c -o ../../../../obj//RecordList.o RecordList.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling ContextJaccard.cpp g++ -c -o ../../../obj//ContextJaccard.o ContextJaccard.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ - Building in src/utils/tabFile * compiling RecordKeyList.cpp * compiling tabFile.cpp g++ -c -o ../../../obj//tabFile.o tabFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//gzstream/ -I../../utils//fileType/ g++ -c -o ../../../../obj//RecordKeyList.o RecordKeyList.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling RecordKeyVector.cpp g++ -c -o ../../../../obj//RecordKeyVector.o RecordKeyVector.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ - Building in src/utils/BamTools * compiling BamAlignment.cpp g++ -c src/api/BamAlignment.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/BamAlignment.o * compiling ContextClosest.cpp g++ -c -o ../../../obj//ContextClosest.o ContextClosest.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling ContextSubtract.cpp g++ -c -o ../../../obj//ContextSubtract.o ContextSubtract.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling GffPlusRecord.cpp g++ -c -o ../../../../obj//GffPlusRecord.o GffPlusRecord.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling ContextCoverage.cpp g++ -c -o ../../../obj//ContextCoverage.o ContextCoverage.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling ContextComplement.cpp g++ -c -o ../../../obj//ContextComplement.o ContextComplement.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ - Building in src/utils/BamTools-Ancillary * compiling BamAncillary.cpp g++ -c -o ../../../obj//BamAncillary.o BamAncillary.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I..//BamTools/include -I..//bedFile/ -I..//lineFileUtilities/ -I..//gzstream/ -I..//fileType/ -Lsrc/utils/BamTools//lib - Building in src/utils/BlockedIntervals * compiling ContextGroupBy.cpp g++ -c -o ../../../obj//ContextGroupBy.o ContextGroupBy.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling BlockedIntervals.cpp g++ -c -o ../../../obj//BlockedIntervals.o BlockedIntervals.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I..//BamTools/include -I..//bedFile/ -I..//gzstream/ -I..//fileType/ -I..//lineFileUtilities/ -Lsrc/utils/BamTools//lib * compiling BamMultiReader.cpp * compiling CloseSweep.cpp g++ -c -o ../../../obj//CloseSweep.o CloseSweep.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//Contexts/ -I../../utils//GenomeFile/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ g++ -c src/api/BamMultiReader.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/BamMultiReader.o * compiling BamReader.cpp g++ -c src/api/BamReader.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/BamReader.o * compiling BamWriter.cpp g++ -c src/api/BamWriter.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/BamWriter.o - Building in src/utils/Fasta * compiling Fasta.cpp g++ -c -o ../../../obj//Fasta.o Fasta.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 * compiling RecordMgr.cpp g++ -c -o ../../../../obj//RecordMgr.o RecordMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ * compiling KeyListOpsMethods.cpp g++ -c -o ../../../obj//KeyListOpsMethods.o KeyListOpsMethods.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//GenomeFile/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling split.cpp g++ -c -o ../../../obj//split.o split.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 - Building in src/utils/VectorOps * compiling VectorOps.cpp g++ -c -o ../../../obj//VectorOps.o VectorOps.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 * compiling BamAncillary.cpp g++ -c -o ../../../obj//BamAncillary.h BamAncillary.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I..//BamTools/include -I..//bedFile/ -I..//lineFileUtilities/ -I..//gzstream/ -I..//fileType/ -Lsrc/utils/BamTools//lib * compiling SamHeader.cpp g++ -c src/api/SamHeader.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamHeader.o * compiling SamProgram.cpp g++ -c src/api/SamProgram.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamProgram.o Fasta.cpp: In member function 'std::__cxx11::string FastaReference::getSequence(std::__cxx11::string)': Fasta.cpp:290:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(seq, sizeof(char), seqlen, file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fasta.cpp: In member function 'std::__cxx11::string FastaReference::getSubSequence(std::__cxx11::string, int, int)': Fasta.cpp:332:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(seq, sizeof(char), (off_t) seqlen, file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling SamProgramChain.cpp g++ -c src/api/SamProgramChain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamProgramChain.o * compiling SamReadGroup.cpp g++ -c src/api/SamReadGroup.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamReadGroup.o - Building in src/utils/GenomeFile * compiling GenomeFile.cpp g++ -c -o ../../../obj//GenomeFile.o GenomeFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I..//general/ -I..//lineFileUtilities/ -I..//KeyListOps/ -I..//BamTools/include/ - Building in src/utils/RecordOutputMgr * compiling RecordOutputMgr.cpp g++ -c -o ../../../obj//RecordOutputMgr.o RecordOutputMgr.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//Contexts/ -I../../utils//GenomeFile/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling SamReadGroupDictionary.cpp g++ -c src/api/SamReadGroupDictionary.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamReadGroupDictionary.o * compiling SamSequence.cpp g++ -c src/api/SamSequence.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamSequence.o * compiling SamSequenceDictionary.cpp g++ -c src/api/SamSequenceDictionary.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamSequenceDictionary.o - Building in src/utils/ToolBase * compiling ToolBase.cpp g++ -c -o ../../../obj//ToolBase.o ToolBase.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//Contexts/ -I../../utils//GenomeFile/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//RecordOutputMgr/ -I../../utils//KeyListOps/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling BamHeader_p.cpp g++ -c src/api/internal/bam/BamHeader_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/bam/BamHeader_p.o GenomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()': GenomeFile.cpp:60:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable] long c2; ^~ * compiling BamMultiReader_p.cpp g++ -c src/api/internal/bam/BamMultiReader_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/bam/BamMultiReader_p.o * compiling BamRandomAccessController_p.cpp g++ -c src/api/internal/bam/BamRandomAccessController_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/bam/BamRandomAccessController_p.o - Building in src/utils/driver * compiling BedtoolsDriver.cpp g++ -c -o ../../../obj//BedtoolsDriver.o BedtoolsDriver.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//bedFile/ -I../../utils//lineFileUtilities/ -I../../utils//Contexts/ -I../../utils//general/ -I../../utils//fileType/ -I../../utils//gzstream/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src -I../../utils//BlockedIntervals -I../../utils//BamTools-Ancillary -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//RecordOutputMgr/ -I../../utils//NewChromsweep -I../../utils//BinTree -I../../utils//ToolBase -I../../utils//version/ -I../../../src//annotateBed/ -I../../../src//bamToBed/ -I../../../src//bamToFastq/ -I../../../src//bedToBam/ -I../../../src//bedpeToBam/ -I../../../src//bedToIgv/ -I../../../src//bed12ToBed6/ -I../../../src//closestFile/ -I../../../src//clusterBed/ -I../../../src//complementFile/ -I../../../src//coverageFile/ -I../../../src//expand/ -I../../../src//fastaFromBed/ -I../../../src//flankBed/ -I../../../src//genomeCoverageBed/ -I../../../src//getOverlap/ -I../../../src//groupBy/ -I../../../src//intersectFile/ -I../../../src//fisher/ -I../../../src//jaccard/ -I../../../src//linksBed/ -I../../../src//maskFastaFromBed/ -I../../../src//mapFile/ -I../../../src//mergeFile/ -I../../../src//multiBamCov/ -I../../../src//multiIntersectBed/ -I../../../src//nekSandbox1/ -I../../../src//nucBed/ -I../../../src//pairToBed/ -I../../../src//pairToPair/ -I../../../src//randomBed/ -I../../../src//regressTest/ -I../../../src//reldist/ -I../../../src//sampleFile/ -I../../../src//shiftBed/ -I../../../src//shuffleBed/ -I../../../src//slopBed/ -I../../../src//sortBed/ -I../../../src//spacingFile/ -I../../../src//split/ -I../../../src//subtractFile/ -I../../../src//tagBam/ -I../../../src//unionBedGraphs/ -I../../../src//windowBed/ -I../../../src//windowMaker/ - Building in src/annotateBed * compiling annotateMain.cpp g++ -c -o ../../obj//annotateMain.o annotateMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//BamTools/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/ - Building in src/bamToBed * compiling bamToBed.cpp g++ -c -o ../../obj//bamToBed.o bamToBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//version/ - Building in src/bamToFastq * compiling bamToFastqMain.cpp g++ -c -o ../../obj//bamToFastqMain.o bamToFastqMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//BamTools/include -I../utils//sequenceUtilities/ -I../utils//version/ * compiling NewGenomeFile.cpp g++ -c -o ../../../obj//NewGenomeFile.o NewGenomeFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I..//general/ -I..//lineFileUtilities/ -I..//KeyListOps/ -I..//BamTools/include/ * compiling BamReader_p.cpp g++ -c src/api/internal/bam/BamReader_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/bam/BamReader_p.o - Building in src/bedToBam - Building in src/bedpeToBam * compiling bedToBam.cpp g++ -c -o ../../obj//bedToBam.o bedToBam.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//version/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/ * compiling bedpeToBam.cpp g++ -c -o ../../obj//bedpeToBam.o bedpeToBam.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//version/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/ * compiling BamWriter_p.cpp g++ -c src/api/internal/bam/BamWriter_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/bam/BamWriter_p.o * compiling BamIndexFactory_p.cpp g++ -c src/api/internal/index/BamIndexFactory_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/index/BamIndexFactory_p.o annotateMain.cpp: In function 'int annotate_main(int, char**)': annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable] bool haveTitles = false; ^~~~~~~~~~ * compiling BamStandardIndex_p.cpp g++ -c src/api/internal/index/BamStandardIndex_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/index/BamStandardIndex_p.o bamToBed.cpp: In function 'int bamtobed_main(int, char**)': bamToBed.cpp:88:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable] bool useAlignmentScore = false; ^~~~~~~~~~~~~~~~~ bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)': bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable] bool haveFastq2 = false; ^~~~~~~~~~ - Building in src/bedToIgv * compiling bedToIgv.cpp g++ -c -o ../../obj//bedToIgv.o bedToIgv.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/ bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)': bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable] bool haveMapQual = false; ^~~~~~~~~~~ * compiling bamToFastq.cpp g++ -c -o ../../obj//bamToFastq.o bamToFastq.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//BamTools/include -I../utils//sequenceUtilities/ -I../utils//version/ bedToBam.cpp: In function 'int bedtobam_main(int, char**)': bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable] bool haveMapQual = false; ^~~~~~~~~~~ * compiling annotateBed.cpp g++ -c -o ../../obj//annotateBed.o annotateBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//BamTools/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/ - Building in src/bed12ToBed6 * compiling bed12ToBed6.cpp g++ -c -o ../../obj//bed12ToBed6.o bed12ToBed6.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//version/ src/api/internal/index/BamStandardIndex_p.cpp: In member function 'void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)': src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'long unsigned int' [-Wsign-compare] if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) ) ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Building in src/closestFile * compiling closestHelp.cpp g++ -c -o ../../obj//closestHelp.o closestHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ - Building in src/clusterBed * compiling BamToolsIndex_p.cpp g++ -c src/api/internal/index/BamToolsIndex_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/index/BamToolsIndex_p.o * compiling clusterMain.cpp g++ -c -o ../../obj//clusterMain.o clusterMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/ * compiling BamDeviceFactory_p.cpp g++ -c src/api/internal/io/BamDeviceFactory_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/BamDeviceFactory_p.o - Building in src/complementFile * compiling complementHelp.cpp g++ -c -o ../../obj//complementHelp.o complementHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ * compiling BamFile_p.cpp g++ -c src/api/internal/io/BamFile_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/BamFile_p.o * compiling BamFtp_p.cpp g++ -c src/api/internal/io/BamFtp_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/BamFtp_p.o * compiling closestFile.cpp g++ -c -o ../../obj//closestFile.o closestFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ clusterMain.cpp: In function 'int cluster_main(int, char**)': clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable] bool haveMaxDistance = false; ^~~~~~~~~~~~~~~ * compiling complementFile.cpp g++ -c -o ../../obj//complementFile.o complementFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ - Building in src/coverageFile * compiling coverageHelp.cpp g++ -c -o ../../obj//coverageHelp.o coverageHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ * compiling BamHttp_p.cpp g++ -c src/api/internal/io/BamHttp_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/BamHttp_p.o - Building in src/expand * compiling expand.cpp g++ -c -o ../../obj//expand.o expand.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//tabFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//VectorOps/ -I../utils//version/ * compiling clusterBed.cpp g++ -c -o ../../obj//clusterBed.o clusterBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/ - Building in src/fastaFromBed * compiling BamPipe_p.cpp g++ -c src/api/internal/io/BamPipe_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/BamPipe_p.o * compiling fastaFromBedMain.cpp g++ -c -o ../../obj//fastaFromBedMain.o fastaFromBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//BamTools/include -I../utils//sequenceUtilities/ -I../utils//BlockedIntervals -I../utils//fileType/ -I../utils//Fasta/ -I../utils//version/ - Building in src/flankBed * compiling flankBedMain.cpp g++ -c -o ../../obj//flankBedMain.o flankBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/ - Building in src/genomeCoverageBed * compiling genomeCoverageMain.cpp g++ -c -o ../../obj//genomeCoverageMain.o genomeCoverageMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//version/ - Building in src/getOverlap * compiling BgzfStream_p.cpp g++ -c src/api/internal/io/BgzfStream_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/BgzfStream_p.o * compiling getOverlap.cpp g++ -c -o ../../obj//getOverlap.o getOverlap.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/ src/api/internal/io/BamHttp_p.cpp: In member function 'bool BamTools::Internal::BamHttp::SendRequest(size_t)': src/api/internal/io/BamHttp_p.cpp:396:63: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] return ( WriteToSocket(requestHeader.c_str(), headerSize) == headerSize ); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ * compiling coverageFile.cpp g++ -c -o ../../obj//coverageFile.o coverageFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ * compiling ByteArray_p.cpp g++ -c src/api/internal/io/ByteArray_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/ByteArray_p.o - Building in src/groupBy * compiling groupBy.cpp g++ -c -o ../../obj//groupBy.o groupBy.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//stringUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ * compiling HostAddress_p.cpp g++ -c src/api/internal/io/HostAddress_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/HostAddress_p.o getOverlap.cpp: In function 'int getoverlap_main(int, char**)': getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable] bool haveColumns = false; ^~~~~~~~~~~ * compiling HostInfo_p.cpp g++ -c src/api/internal/io/HostInfo_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/HostInfo_p.o * compiling HttpHeader_p.cpp g++ -c src/api/internal/io/HttpHeader_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/HttpHeader_p.o * compiling ILocalIODevice_p.cpp g++ -c src/api/internal/io/ILocalIODevice_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/ILocalIODevice_p.o - Building in src/intersectFile * compiling intersectHelp.cpp g++ -c -o ../../obj//intersectHelp.o intersectHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//ToolBase -I../utils//version/ src/api/internal/io/HostAddress_p.cpp: In member function 'void BamTools::Internal::HostAddress::Clear()': src/api/internal/io/HostAddress_p.cpp:283:49: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct BamTools::Internal::IPv6Address'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&m_ip6Address, 0, sizeof(IPv6Address)); ^ In file included from src/api/internal/io/HostAddress_p.cpp:10: src/api/internal/io/HostAddress_p.h:30:8: note: 'struct BamTools::Internal::IPv6Address' declared here struct IPv6Address { ^~~~~~~~~~~ src/api/internal/io/HostAddress_p.cpp: In member function 'std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const': src/api/internal/io/HostAddress_p.cpp:325:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if ( i != 0 ) ^~ src/api/internal/io/HostAddress_p.cpp:327:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) | ^~ * compiling intersectFile.cpp g++ -c -o ../../obj//intersectFile.o intersectFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//ToolBase -I../utils//version/ coverageFile.cpp: In member function 'virtual void CoverageFile::giveFinalReport(RecordOutputMgr*)': coverageFile.cpp:100:11: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] asprintf(&depthPctString, "%0.7f", depthPct); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coverageFile.cpp: In member function 'void CoverageFile::doMean(RecordOutputMgr*, RecordKeyVector&)': coverageFile.cpp:181:10: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] asprintf(&meanString, "%0.7f", mean); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ coverageFile.cpp: In member function 'void CoverageFile::doHist(RecordOutputMgr*, RecordKeyVector&)': coverageFile.cpp:210:11: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] asprintf(&coveredFractionString, "%0.7f", coveredFraction); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coverageFile.cpp: In member function 'void CoverageFile::doDefault(RecordOutputMgr*, RecordKeyVector&)': coverageFile.cpp:230:10: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] asprintf(&coveredFractionString, "%0.7f", coveredFraction); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling fastaFromBed.cpp g++ -c -o ../../obj//fastaFromBed.o fastaFromBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//BamTools/include -I../utils//sequenceUtilities/ -I../utils//BlockedIntervals -I../utils//fileType/ -I../utils//Fasta/ -I../utils//version/ - Building in src/fisher * compiling fisherHelp.cpp g++ -c -o ../../obj//fisherHelp.o fisherHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//gzstream/ -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I . -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ -I../../src//jaccard/ * compiling RollingBuffer_p.cpp g++ -c src/api/internal/io/RollingBuffer_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/RollingBuffer_p.o * compiling TcpSocketEngine_p.cpp g++ -c src/api/internal/io/TcpSocketEngine_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/TcpSocketEngine_p.o * compiling TcpSocketEngine_unix_p.cpp g++ -c src/api/internal/io/TcpSocketEngine_unix_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/TcpSocketEngine_unix_p.o * compiling TcpSocket_p.cpp g++ -c src/api/internal/io/TcpSocket_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/TcpSocket_p.o * compiling flankBed.cpp g++ -c -o ../../obj//flankBed.o flankBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/ * compiling SamFormatParser_p.cpp g++ -c src/api/internal/sam/SamFormatParser_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/sam/SamFormatParser_p.o - Building in src/jaccard * compiling jaccardHelp.cpp g++ -c -o ../../obj//jaccardHelp.o jaccardHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ intersectFile.cpp: In member function 'virtual void IntersectFile::processHits(RecordOutputMgr*, RecordKeyVector&)': intersectFile.cpp:70:33: warning: variable 'hitListIter' set but not used [-Wunused-but-set-variable] RecordKeyVector::iterator_type hitListIter = hits.begin(); ^~~~~~~~~~~ - Building in src/linksBed * compiling linksMain.cpp g++ -c -o ../../obj//linksMain.o linksMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/ * compiling fisher.cpp g++ -c -o ../../obj//fisher.o fisher.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//gzstream/ -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I . -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ -I../../src//jaccard/ * compiling SamFormatPrinter_p.cpp g++ -c src/api/internal/sam/SamFormatPrinter_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/sam/SamFormatPrinter_p.o - Building in src/maskFastaFromBed * compiling maskFastaFromBedMain.cpp g++ -c -o ../../obj//maskFastaFromBedMain.o maskFastaFromBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//sequenceUtilities/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Fasta/ -I../utils//version/ * compiling jaccard.cpp g++ -c -o ../../obj//jaccard.o jaccard.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ - Building in src/mapFile * compiling mapHelp.cpp g++ -c -o ../../obj//mapHelp.o mapHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ * compiling genomeCoverageBed.cpp g++ -c -o ../../obj//genomeCoverageBed.o genomeCoverageBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//version/ * compiling SamHeaderValidator_p.cpp g++ -c src/api/internal/sam/SamHeaderValidator_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/sam/SamHeaderValidator_p.o * compiling groupByHelp.cpp g++ -c -o ../../obj//groupByHelp.o groupByHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//stringUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ * compiling BamException_p.cpp g++ -c src/api/internal/utils/BamException_p.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/utils/BamException_p.o - Building in src/mergeFile * compiling mergeHelp.cpp g++ -c -o ../../obj//mergeHelp.o mergeHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ - Building in src/multiBamCov * compiling multiBamCovMain.cpp g++ -c -o ../../obj//multiBamCovMain.o multiBamCovMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//version/ - Building in src/multiIntersectBed * compiling multiIntersectBedMain.cpp g++ -c -o ../../obj//multiIntersectBedMain.o multiIntersectBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//GenomeFile/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Point/ -I../utils//BamTools/include -I../utils//version/ genomeCoverageBed.cpp: In member function 'void BedGenomeCoverage::CoverageBam(std::__cxx11::string)': genomeCoverageBed.cpp:322:23: warning: comparison of integer expressions of different signedness: 'CHRPOS' {aka 'unsigned int'} and 'int' [-Wsign-compare] if(end<_fragmentSize) { //sometimes fragmentSize is bigger :( ~~~^~~~~~~~~~~~~~ * compiling mapFile.cpp g++ -c -o ../../obj//mapFile.o mapFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)': multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable] bool haveBed = false; ^~~~~~~ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable] bool haveBams = false; ^~~~~~~~ multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ * compiling linksBed.cpp g++ -c -o ../../obj//linksBed.o linksBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/ - Building in src/nucBed * compiling nucBedMain.cpp g++ -c -o ../../obj//nucBedMain.o nucBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//sequenceUtilities/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Fasta/ -I../utils//version/ * compiling mergeFile.cpp g++ -c -o ../../obj//mergeFile.o mergeFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ * compiling kfunc.cpp g++ -c -o ../../obj//kfunc.o kfunc.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//gzstream/ -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//RecordOutputMgr/ -I../utils//KeyListOps/ -I../utils//NewChromsweep -I../utils//VectorOps -I . -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ -I../../src//jaccard/ * compiling maskFastaFromBed.cpp g++ -c -o ../../obj//maskFastaFromBed.o maskFastaFromBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//sequenceUtilities/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Fasta/ -I../utils//version/ - Building in src/pairToBed * compiling pairToBedMain.cpp g++ -c -o ../../obj//pairToBedMain.o pairToBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFilePE/ -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/ - Building in src/pairToPair * compiling pairToPairMain.cpp g++ -c -o ../../obj//pairToPairMain.o pairToPairMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFilePE/ -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//version/ -I../utils//fileType/ -I../utils//version/ - Building in src/randomBed * compiling randomBedMain.cpp g++ -c -o ../../obj//randomBedMain.o randomBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//version/ multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)': multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable] bool haveFiles = false; ^~~~~~~~~ multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable] bool haveGenome = false; ^~~~~~~~~~ multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] bool haveFiller = true; ^~~~~~~~~~ * compiling randomBed.cpp g++ -c -o ../../obj//randomBed.o randomBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//version/ - Building in src/regressTest compiling RegressTest.cpp g++ -c -o ../../obj//RegressTest.o RegressTest.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general - Building in src/reldist * compiling reldistMain.cpp g++ -c -o ../../obj//reldistMain.o reldistMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//chromsweep -I../utils//version/ * compiling multiBamCov.cpp g++ -c -o ../../obj//multiBamCov.o multiBamCov.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//version/ - Building in src/sampleFile * compiling sampleHelp.cpp g++ -c -o ../../obj//sampleHelp.o sampleHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//version/ -I../utils//ToolBase/ pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)': pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)': pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ * compiling pairToPair.cpp g++ -c -o ../../obj//pairToPair.o pairToPair.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFilePE/ -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//version/ -I../utils//fileType/ -I../utils//version/ * compiling multiIntersectBed.cpp g++ -c -o ../../obj//multiIntersectBed.o multiIntersectBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//GenomeFile/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Point/ -I../utils//BamTools/include -I../utils//version/ * compiling sampleFile.cpp g++ -c -o ../../obj//sampleFile.o sampleFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//version/ -I../utils//ToolBase/ * compiling nucBed.cpp g++ -c -o ../../obj//nucBed.o nucBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//sequenceUtilities/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Fasta/ -I../utils//version/ * linking lib/libbamtools.a ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o - Building in src/shiftBed * compiling shiftBedMain.cpp g++ -c -o ../../obj//shiftBedMain.o shiftBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/ ranlib lib/libbamtools.a - Building in src/shuffleBed - Building in src/slopBed * compiling shuffleBedMain.cpp g++ -c -o ../../obj//shuffleBedMain.o shuffleBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/ RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)': RegressTest.cpp:431:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(diffCmd.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function 'bool RegressTest::startMemoryProfile(bool)': RegressTest.cpp:573:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ * compiling slopBedMain.cpp g++ -c -o ../../obj//slopBedMain.o slopBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/ RegressTest.cpp: In member function 'bool RegressTest::calcMemoryStats()': RegressTest.cpp:622:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ * compiling reldist.cpp g++ -c -o ../../obj//reldist.o reldist.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//chromsweep -I../utils//version/ - Building in src/sortBed * compiling sortMain.cpp g++ -c -o ../../obj//sortMain.o sortMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/ * compiling shuffleBed.cpp g++ -c -o ../../obj//shuffleBed.o shuffleBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/ pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)': pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable] bool found1 = false; ^~~~~~ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable] bool found2 = false; ^~~~~~ - Building in src/spacingFile * compiling spacingHelp.cpp g++ -c -o ../../obj//spacingHelp.o spacingHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//version/ -I../utils//ToolBase/ * compiling pairToBed.cpp g++ -c -o ../../obj//pairToBed.o pairToBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFilePE/ -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/ - Building in src/split * compiling splitBed.cpp g++ -c -o ../../obj//splitBed.o splitBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/ - Building in src/subtractFile * compiling subtractHelp.cpp g++ -c -o ../../obj//subtractHelp.o subtractHelp.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ * compiling spacingFile.cpp g++ -c -o ../../obj//spacingFile.o spacingFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//version/ -I../utils//ToolBase/ * compiling sortBed.cpp g++ -c -o ../../obj//sortBed.o sortBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/ pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector&, const string&)': pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] CHRPOS spanLength = 0; ^~~~~~~~~~ pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)': pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] int spanLength = 0; ^~~~~~~~~~ - Building in src/tagBam * compiling slopBed.cpp * compiling tagBamMain.cpp g++ -c -o ../../obj//slopBed.o slopBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/ g++ -c -o ../../obj//tagBamMain.o tagBamMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/ * compiling shiftBed.cpp g++ -c -o ../../obj//shiftBed.o shiftBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/ - Building in src/unionBedGraphs * compiling subtractFile.cpp g++ -c -o ../../obj//subtractFile.o subtractFile.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ * compiling unionBedGraphsMain.cpp g++ -c -o ../../obj//unionBedGraphsMain.o unionBedGraphsMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedGraphFile/ -I../utils//lineFileUtilities/ -I../utils//GenomeFile/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Point/ -I../utils//BamTools/include -I../utils//version/ * compiling splitBedMain.cpp g++ -c -o ../../obj//splitBedMain.o splitBedMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/ - Building in src/windowBed * compiling windowMain.cpp g++ -c -o ../../obj//windowMain.o windowMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/ - Building in src/windowMaker * compiling windowMakerMain.cpp g++ -c -o ../../obj//windowMakerMain.o windowMakerMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//GenomeFile/ -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//BamTools/include -I../utils//version/ unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)': unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable] bool haveFiles = false; ^~~~~~~~~ unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable] bool haveGenome = false; ^~~~~~~~~~ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] bool haveFiller = true; ^~~~~~~~~~ * compiling windowMaker.cpp g++ -c -o ../../obj//windowMaker.o windowMaker.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//GenomeFile/ -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//BamTools/include -I../utils//version/ * compiling tagBam.cpp g++ -c -o ../../obj//tagBam.o tagBam.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/ compiling regressTestMain.cpp g++ -c -o ../../obj//regressTestMain.o regressTestMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general * compiling windowBed.cpp g++ -c -o ../../obj//windowBed.o windowBed.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/ * compiling unionBedGraphs.cpp g++ -c -o ../../obj//unionBedGraphs.o unionBedGraphs.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedGraphFile/ -I../utils//lineFileUtilities/ -I../utils//GenomeFile/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Point/ -I../utils//BamTools/include -I../utils//version/ - Building main bedtools binary. done. - Creating executables for old CLI. done. make[1]: Leaving directory '/build/bedtools-2.27.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/bedtools-2.27.1+dfsg' dh_auto_test make -j15 test make[2]: Entering directory '/build/bedtools-2.27.1+dfsg' $CXXFLAGS is [-g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11] Building BEDTools: ========================================================= * Creating BamTools API DETECTED_VERSION = v2.27.1 CURRENT_VERSION = v2.27.1 - Building in src/utils/FileRecordTools - Building in src/utils/FileRecordTools/FileReaders - Building in FileReaders - Building in src/utils/FileRecordTools/Records make[3]: Nothing to be done for 'all'. make[4]: Nothing to be done for 'all'. - Building in Records - Building in src/utils/bedFile make[3]: Nothing to be done for 'all'. - Building in src/utils/BinTree make[3]: '../../../obj//bedFile.o' is up to date. make[4]: Nothing to be done for 'all'. - Building in src/utils/version make[3]: '../../../obj//BinTree.o' is up to date. - Building in src/utils/bedGraphFile make[3]: '../../../obj//bedGraphFile.o' is up to date. make[3]: Nothing to be done for 'all'. - Building in src/utils/chromsweep - Building in src/utils/Contexts make[3]: '../../../obj//chromsweep.o' is up to date. - Building in src/utils/general make[3]: Nothing to be done for 'all'. - Building in src/utils/gzstream make[3]: Nothing to be done for 'all'. - Building in src/utils/fileType make[3]: '../../../obj//gzstream.o' is up to date. - Building in src/utils/bedFilePE make[3]: Nothing to be done for 'all'. - Building in src/utils/KeyListOps - Building in src/utils/NewChromsweep make[3]: '../../../obj//bedFilePE.o' is up to date. make[3]: Nothing to be done for 'all'. - Building in src/utils/sequenceUtilities make[3]: Nothing to be done for 'all'. - Building in src/utils/tabFile make[3]: '../../../obj//sequenceUtils.o' is up to date. - Building in src/utils/BamTools make[3]: '../../../obj//tabFile.o' is up to date. - Building in src/utils/BamTools-Ancillary make[3]: Nothing to be done for 'all'. - Building in src/utils/BlockedIntervals make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/utils/Fasta - Building in src/utils/VectorOps make[3]: Nothing to be done for 'all'. - Building in src/utils/GenomeFile make[3]: '../../../obj//VectorOps.o' is up to date. - Building in src/utils/RecordOutputMgr make[3]: '../../../obj//NewGenomeFile.o' is up to date. make[3]: '../../../obj//RecordOutputMgr.o' is up to date. - Building in src/utils/ToolBase - Building in src/utils/driver - Building in src/annotateBed - Building in src/bamToBed make[3]: Nothing to be done for 'all'. make[3]: '../../../obj//ToolBase.o' is up to date. make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/bamToFastq - Building in src/bedToBam make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/bedpeToBam - Building in src/bedToIgv make[3]: Nothing to be done for 'all'. - Building in src/bed12ToBed6 make[3]: Nothing to be done for 'all'. - Building in src/closestFile make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/clusterBed - Building in src/complementFile make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/coverageFile - Building in src/expand make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/fastaFromBed - Building in src/flankBed make[3]: Nothing to be done for 'all'. - Building in src/genomeCoverageBed make[3]: Nothing to be done for 'all'. - Building in src/getOverlap - Building in src/groupBy make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/fisher - Building in src/intersectFile make[3]: Nothing to be done for 'all'. - Building in src/jaccard make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/maskFastaFromBed make[3]: Nothing to be done for 'all'. - Building in src/linksBed - Building in src/mapFile make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/mergeFile make[3]: Nothing to be done for 'all'. - Building in src/multiBamCov make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/nucBed - Building in src/multiIntersectBed - Building in src/pairToBed make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/pairToPair make[3]: Nothing to be done for 'all'. - Building in src/randomBed make[3]: Nothing to be done for 'all'. - Building in src/regressTest - Building in src/reldist - Building in src/sampleFile make[3]: Nothing to be done for 'all'. compiling RegressTest.cpp g++ -c -o ../../obj//RegressTest.o RegressTest.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general make[3]: Nothing to be done for 'all'. - Building in src/shiftBed - Building in src/shuffleBed make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/slopBed make[3]: Nothing to be done for 'all'. - Building in src/sortBed - Building in src/spacingFile make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/split make[3]: Nothing to be done for 'all'. - Building in src/subtractFile - Building in src/tagBam make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/unionBedGraphs - Building in src/windowBed make[3]: Nothing to be done for 'all'. - Building in src/windowMaker make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)': RegressTest.cpp:431:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(diffCmd.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function 'bool RegressTest::startMemoryProfile(bool)': RegressTest.cpp:573:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function 'bool RegressTest::calcMemoryStats()': RegressTest.cpp:622:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ compiling regressTestMain.cpp g++ -c -o ../../obj//regressTestMain.o regressTestMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general - Building main bedtools binary. done. - Creating executables for old CLI. done. 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 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 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...ok kclosest.t12...ok kclosest.t13...ok kclosest.t14...ok kclosest.t15...ok kclosest.t16...ok kclosest.t17...ok kclosest.t18...ok kclosest.t19...ok kclosest.t20...ok kclosest.t21...ok kclosest.t22...ok kclosest.t23...ok kclosest.t24...ok kclosest.t25...ok kclosest.t26...ok kclosest.t27...ok kclosest.t28...ok kclosest.t29...ok kclosest.t30...ok kclosest.t31...ok kclosest.t32...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 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 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 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...index file test.iupac.fa.fai not found, generating... ok getfasta.t09...index file test.iupac.fa.fai not found, generating... ok getfasta.t10...index file test.fa.fai not found, generating... ok getfasta.t11...ok getfasta.t12...ok getfasta.t13...ok getfasta.t14...ok getfasta.t15...ok getfasta.t134..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.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.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 ########################################################### # # 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.t13...ok intersect.t14...ok intersect.t15...ok intersect.t16...ok intersect.t17...ok intersect.t18...ok intersect.t19...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 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 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 Testing bedtools negativecontrol: Testing bedtools reldist: reldist.t01...ok reldist.t02...ok reldist.t03...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 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 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/bedtools-2.27.1+dfsg' make[1]: Leaving directory '/build/bedtools-2.27.1+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot 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/ dh_auto_install install -d /build/bedtools-2.27.1\+dfsg/debian/tmp make -j15 install DESTDIR=/build/bedtools-2.27.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bedtools-2.27.1+dfsg' $CXXFLAGS is [-g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11] Building BEDTools: ========================================================= * Creating BamTools API DETECTED_VERSION = v2.27.1 CURRENT_VERSION = v2.27.1 - Building in src/utils/FileRecordTools - Building in src/utils/FileRecordTools/FileReaders - Building in src/utils/FileRecordTools/Records - Building in src/utils/bedFile - Building in src/utils/BinTree - Building in src/utils/bedGraphFile - Building in src/utils/version - Building in src/utils/chromsweep - Building in src/utils/Contexts - Building in src/utils/general - Building in src/utils/gzstream - Building in src/utils/fileType - Building in src/utils/bedFilePE - Building in src/utils/KeyListOps - Building in src/utils/NewChromsweep make[2]: '../../../obj//BinTree.o' is up to date. make[2]: '../../../obj//bedFile.o' is up to date. make[2]: '../../../obj//bedGraphFile.o' is up to date. make[2]: '../../../obj//chromsweep.o' is up to date. make[2]: Nothing to be done for 'all'. make[2]: '../../../obj//gzstream.o' is up to date. - Building in FileReaders - Building in src/utils/sequenceUtilities - Building in src/utils/tabFile make[2]: '../../../obj//bedFilePE.o' is up to date. - Building in src/utils/BamTools make[2]: Nothing to be done for 'all'. - Building in src/utils/BamTools-Ancillary - Building in src/utils/BlockedIntervals make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in src/utils/Fasta make[2]: Nothing to be done for 'all'. - Building in src/utils/VectorOps - Building in src/utils/GenomeFile - Building in src/utils/RecordOutputMgr - Building in src/utils/ToolBase - Building in src/utils/driver make[2]: Nothing to be done for 'all'. make[2]: '../../../obj//sequenceUtils.o' is up to date. make[2]: '../../../obj//tabFile.o' is up to date. - Building in src/annotateBed make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. make[2]: '../../../obj//VectorOps.o' is up to date. - Building in src/bamToBed - Building in src/bamToFastq - Building in Records make[2]: Nothing to be done for 'all'. make[2]: '../../../obj//ToolBase.o' is up to date. - Building in src/bedToBam - Building in src/bedpeToBam make[2]: '../../../obj//RecordOutputMgr.o' is up to date. make[2]: '../../../obj//NewGenomeFile.o' is up to date. make[2]: Nothing to be done for 'all'. - Building in src/bedToIgv - Building in src/bed12ToBed6 - Building in src/closestFile - Building in src/clusterBed - Building in src/complementFile - Building in src/coverageFile make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in src/expand - Building in src/fastaFromBed make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in src/flankBed make[2]: Nothing to be done for 'all'. - Building in src/genomeCoverageBed make[2]: Nothing to be done for 'all'. - Building in src/getOverlap - Building in src/groupBy - Building in src/intersectFile - Building in src/fisher make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in src/jaccard make[2]: Nothing to be done for 'all'. - Building in src/linksBed - Building in src/maskFastaFromBed - Building in src/mapFile - Building in src/mergeFile make[2]: Nothing to be done for 'all'. - Building in src/multiBamCov make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in src/multiIntersectBed make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in src/nucBed - Building in src/pairToPair - Building in src/pairToBed make[2]: Nothing to be done for 'all'. - Building in src/randomBed - Building in src/regressTest make[3]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in src/reldist - Building in src/sampleFile - Building in src/shiftBed make[2]: Nothing to be done for 'all'. - Building in src/shuffleBed - Building in src/slopBed - Building in src/sortBed - Building in src/spacingFile make[2]: Nothing to be done for 'all'. - Building in src/split make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in src/subtractFile compiling RegressTest.cpp g++ -c -o ../../obj//RegressTest.o RegressTest.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general - Building in src/tagBam make[2]: Nothing to be done for 'all'. - Building in src/unionBedGraphs - Building in src/windowBed make[2]: Nothing to be done for 'all'. - Building in src/windowMaker make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)': RegressTest.cpp:431:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(diffCmd.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function 'bool RegressTest::startMemoryProfile(bool)': RegressTest.cpp:573:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function 'bool RegressTest::calcMemoryStats()': RegressTest.cpp:622:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ compiling regressTestMain.cpp g++ -c -o ../../obj//regressTestMain.o regressTestMain.cpp -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -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 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general - Building main bedtools binary. done. - Creating executables for old CLI. done. mkdir -p /build/bedtools-2.27.1+dfsg/debian/tmp/usr/local/bin for file in bin/* ; do \ cp -f $file /build/bedtools-2.27.1+dfsg/debian/tmp/usr/local/bin; \ done make[1]: Leaving directory '/build/bedtools-2.27.1+dfsg' rm -f debian/bedtools-test.debhelper.log debian/bedtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/bedtools-2.27.1+dfsg' dh_install install -d debian/bedtools//usr/share/bash-completion/completions cp --reflink=auto -a ./debian/bash_completion/bedtools debian/bedtools//usr/share/bash-completion/completions/ install -d debian/bedtools/usr/bin cp --reflink=auto -a ./bin/annotateBed ./bin/bamToBed ./bin/bamToFastq ./bin/bed12ToBed6 ./bin/bedToBam ./bin/bedToIgv ./bin/bedpeToBam ./bin/bedtools ./bin/closestBed ./bin/clusterBed ./bin/complementBed ./bin/coverageBed ./bin/expandCols ./bin/fastaFromBed ./bin/flankBed ./bin/genomeCoverageBed ./bin/getOverlap ./bin/groupBy ./bin/intersectBed ./bin/linksBed ./bin/mapBed ./bin/maskFastaFromBed ./bin/mergeBed ./bin/multiBamCov ./bin/multiIntersectBed ./bin/nucBed ./bin/pairToBed ./bin/pairToPair ./bin/randomBed ./bin/shiftBed ./bin/shuffleBed ./bin/slopBed ./bin/sortBed ./bin/subtractBed ./bin/tagBam ./bin/unionBedGraphs ./bin/windowBed ./bin/windowMaker debian/bedtools/usr/bin/ install -d debian/bedtools/usr/share/bedtools cp --reflink=auto -a ./genomes debian/bedtools/usr/share/bedtools/ install -d debian/.debhelper/generated/bedtools install -d debian/bedtools-test/usr/share/bedtools/test cp --reflink=auto -a ./test/intersect debian/bedtools-test/usr/share/bedtools/test/ cp --reflink=auto -a ./debian/test_missing_files/intersect debian/bedtools-test/usr/share/bedtools/test/ install -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/ cp --reflink=auto -a ./test/bamtobed ./test/bamtofastq ./test/bed12tobed6 ./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/ install -d debian/.debhelper/generated/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/bedtools-2.27.1+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/bedtools-2.27.1+dfsg' dh_installdocs install -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 chown -R 0:0 debian/bedtools/usr/share/doc chmod -R u\+rw,go=rX debian/bedtools/usr/share/doc install -p -m0644 debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright install -d debian/bedtools-test/usr/share/doc/bedtools-test install -p -m0644 debian/copyright debian/bedtools-test/usr/share/doc/bedtools-test/copyright rm -f debian/bedtools-test.debhelper.log debian/bedtools.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/bedtools-2.27.1+dfsg' dh_installchangelogs RELEASE_HISTORY install -p -m0644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian install -p -m0644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog install -p -m0644 debian/changelog debian/bedtools-test/usr/share/doc/bedtools-test/changelog.Debian install -p -m0644 RELEASE_HISTORY debian/bedtools-test/usr/share/doc/bedtools-test/changelog make[1]: Leaving directory '/build/bedtools-2.27.1+dfsg' dh_perl dh_link dh_strip_nondeterminism Using 1550149881 as canonical time Normalizing debian/bedtools-test/usr/share/bedtools/data/refseq.chr1.exons.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/test/general/non-empty.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/data/simpleRepeats.chr1.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/test/intersect/bug44_a.vcf.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/test/intersect/a_gzipped.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/test/intersect/a_withLargeHeader_gzipped.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/test/intersect/a_bgzipped.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/test/intersect/a_withLargeHeader_bgzipped.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/data/gerp.chr1.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/data/aluY.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 usr/share/doc/bedtools-test/changelog.Debian chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian gzip -9nf usr/share/doc/bedtools-test/changelog usr/share/doc/bedtools-test/changelog.Debian gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian cd '/build/bedtools-2.27.1+dfsg' cd '/build/bedtools-2.27.1+dfsg' rm -f debian/bedtools-test.debhelper.log debian/bedtools.debhelper.log debian/rules override_dh_fixperms-arch make[1]: Entering directory '/build/bedtools-2.27.1+dfsg' dh_fixperms find debian/bedtools -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 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/bedtools-2.27.1+dfsg/debian/bedtools/usr/share/bedtools/genomes/*.genome find /build/bedtools-2.27.1+dfsg/debian -name "*.bed" -executable -exec chmod -x \{\} \; find /build/bedtools-2.27.1+dfsg/debian -name "*.sh" -not -executable -exec chmod +x \{\} \; make[1]: Leaving directory '/build/bedtools-2.27.1+dfsg' dh_fixperms -Nbedtools find debian/bedtools-test -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 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_strip install -d debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/af objcopy --only-keep-debug --compress-debug-sections debian/bedtools/usr/bin/bedtools debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/af/9cdb19a2c8d6eac6ba8ee31d21d627f228449d.debug chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/af/9cdb19a2c8d6eac6ba8ee31d21d627f228449d.debug chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/af/9cdb19a2c8d6eac6ba8ee31d21d627f228449d.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/af/9cdb19a2c8d6eac6ba8ee31d21d627f228449d.debug debian/bedtools/usr/bin/bedtools install -d debian/.debhelper/bedtools/dbgsym-root/usr/share/doc ln -s bedtools debian/.debhelper/bedtools/dbgsym-root/usr/share/doc/bedtools-dbgsym dh_makeshlibs rm -f debian/bedtools/DEBIAN/shlibs rm -f debian/bedtools-test/DEBIAN/shlibs dh_shlibdeps install -d debian/bedtools/DEBIAN dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools dh_installdeb install -d debian/bedtools-test/DEBIAN dh_gencontrol 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 -Pdebian/bedtools-test echo misc:Depends= >> debian/bedtools.substvars echo misc:Pre-Depends= >> debian/bedtools.substvars install -d debian/.debhelper/bedtools/dbgsym-root/DEBIAN dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/.debhelper/bedtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=bedtools-dbgsym "-DDepends=bedtools (= \${binary:Version})" "-DDescription=debug symbols for bedtools" -DBuild-Ids=af9cdb19a2c8d6eac6ba8ee31d21d627f228449d -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools -UMulti-Arch chmod 0644 -- debian/bedtools-test/DEBIAN/control chown 0:0 -- debian/bedtools-test/DEBIAN/control chmod 0644 -- debian/bedtools/DEBIAN/control chown 0:0 -- debian/bedtools/DEBIAN/control dh_md5sums cd debian/bedtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/bedtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/bedtools/DEBIAN/md5sums chown 0:0 -- debian/bedtools/DEBIAN/md5sums cd debian/.debhelper/bedtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/bedtools-test/DEBIAN/md5sums chown 0:0 -- debian/bedtools-test/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/bedtools .. dpkg-deb --build debian/.debhelper/bedtools/dbgsym-root .. dpkg-deb --build debian/bedtools-test .. dpkg-deb: building package 'bedtools-dbgsym' in '../bedtools-dbgsym_2.27.1+dfsg-4_amd64.deb'. dpkg-deb: building package 'bedtools' in '../bedtools_2.27.1+dfsg-4_amd64.deb'. dpkg-deb: building package 'bedtools-test' in '../bedtools-test_2.27.1+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bedtools_2.27.1+dfsg-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from bedtools-2.27.1+dfsg/debian/source/options: --single-debian-patch dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/29987/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/29987/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/29987 and its subdirectories I: Current time: Mon Aug 16 04:10:21 +14 2021 I: pbuilder-time-stamp: 1629036621