Diff of the two buildlogs: -- --- b1/build.log 2020-08-10 08:59:50.164197421 +0000 +++ b2/build.log 2020-08-10 09:11:41.222336649 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Aug 9 20:30:22 -12 2020 -I: pbuilder-time-stamp: 1597048222 +I: Current time: Mon Aug 10 23:00:29 +14 2020 +I: pbuilder-time-stamp: 1597050029 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Thu Feb 14 01:14:15 2019 -12 +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 @@ -33,136 +33,170 @@ dpkg-source: info: applying flag_no_overwrite I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/13845/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/26160/tmp/hooks/D01_modify_environment starting +debug: Running on jtx1c. +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/26160/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/26160/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='7763b0dede8845c5989b8402e7d26ec5' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='13845' - PS1='# ' - PS2='> ' + INVOCATION_ID=9dbfccc02d5a45f2a3abe88154565137 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=26160 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.37KqvOYac9/pbuilderrc_3VqD --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.37KqvOYac9/b1 --logfile b1/build.log bedtools_2.27.1+dfsg-4.dsc' - SUDO_GID='114' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.37KqvOYac9/pbuilderrc_09oW --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.37KqvOYac9/b2 --logfile b2/build.log bedtools_2.27.1+dfsg-4.dsc' + SUDO_GID=111 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux jtk1b 4.19.0-10-armmp-lpae #1 SMP Debian 4.19.132-1 (2020-07-24) armv7l GNU/Linux + Linux i-capture-the-hostname 4.19.0-10-arm64 #1 SMP Debian 4.19.132-1 (2020-07-24) aarch64 GNU/Linux I: ls -l /bin total 3328 - -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat - -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown - -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp - -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash - -rwxr-xr-x 1 root root 71648 Feb 28 2019 date - -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd - -rwxr-xr-x 1 root root 55672 Feb 28 2019 df - -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir - -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 18260 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount - -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln - -rwxr-xr-x 1 root root 34932 Jul 26 2018 login - -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls - -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 26024 Jan 9 2019 more - -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount - -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm - -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 8 20:28 sh -> dash - -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty - -rwsr-xr-x 1 root root 42472 Jan 9 2019 su - -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync - -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar - -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch - -rwxr-xr-x 1 root root 18260 Feb 28 2019 true - -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server - -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount - -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/13845/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 767656 Apr 18 2019 bash + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 26052 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 26052 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 9636 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 22432 Mar 1 2019 cat + -rwxr-xr-x 1 root root 38868 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 38836 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 42972 Mar 1 2019 chown + -rwxr-xr-x 1 root root 88376 Mar 1 2019 cp + -rwxr-xr-x 1 root root 75516 Jan 18 2019 dash + -rwxr-xr-x 1 root root 71648 Mar 1 2019 date + -rwxr-xr-x 1 root root 51212 Mar 1 2019 dd + -rwxr-xr-x 1 root root 55672 Mar 1 2019 df + -rwxr-xr-x 1 root root 88444 Mar 1 2019 dir + -rwxr-xr-x 1 root root 54872 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 22364 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 18260 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 47356 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 21980 Apr 23 09:38 fusermount + -rwxr-xr-x 1 root root 124508 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 64232 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 13784 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 43044 Mar 1 2019 ln + -rwxr-xr-x 1 root root 34932 Jul 27 2018 login + -rwxr-xr-x 1 root root 88444 Mar 1 2019 ls + -rwxr-xr-x 1 root root 67036 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 47168 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 43040 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 26552 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 26024 Jan 10 2019 more + -rwsr-xr-x 1 root root 34268 Jan 10 2019 mount + -rwxr-xr-x 1 root root 9688 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 84284 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 22416 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 26504 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 42968 Mar 1 2019 rm + -rwxr-xr-x 1 root root 26496 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 14136 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 10 23:00 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 9 22:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 22384 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 51124 Mar 1 2019 stty + -rwsr-xr-x 1 root root 42472 Jan 10 2019 su + -rwxr-xr-x 1 root root 22392 Mar 1 2019 sync + -rwxr-xr-x 1 root root 283324 Apr 24 2019 tar + -rwxr-xr-x 1 root root 9808 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 63464 Mar 1 2019 touch + -rwxr-xr-x 1 root root 18260 Mar 1 2019 true + -rwxr-xr-x 1 root root 9636 Apr 23 09:38 ulockmgr_server + -rwsr-xr-x 1 root root 21976 Jan 10 2019 umount + -rwxr-xr-x 1 root root 22380 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 88444 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 21980 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/26160/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -270,7 +304,7 @@ Get: 64 http://deb.debian.org/debian buster/main armhf libhts2 armhf 1.9-11 [261 kB] Get: 65 http://deb.debian.org/debian buster/main armhf samtools armhf 1.9-4 [410 kB] Get: 66 http://deb.debian.org/debian buster/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB] -Fetched 26.3 MB in 4s (6364 kB/s) +Fetched 26.3 MB in 17s (1523 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) @@ -559,7 +593,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/bedtools-2.27.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +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 @@ -570,7 +604,7 @@ fakeroot debian/rules clean dh clean dh_auto_clean - make -j3 clean + make -j4 clean make[1]: Entering directory '/build/bedtools-2.27.1+dfsg' * Cleaning-up BamTools API * Cleaning up. @@ -594,7 +628,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j3 "INSTALL=install --strip-program=true" + make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/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: @@ -605,13 +639,16 @@ Updating version file. - Building in src/utils/FileRecordTools - Building in src/utils/FileRecordTools/FileReaders - * compiling FileRecordMgr.cpp - Building in src/utils/FileRecordTools/Records -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/ +- Building in src/utils/bedFile + * compiling FileRecordMgr.cpp * 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 Record.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//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/ 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/ + * compiling bedFile.cpp +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/ * 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 EmptyRecord.cpp @@ -622,39 +659,6 @@ 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 BamFileReader.cpp 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 FileRecordMgr.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/ - * 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 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/ - * 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 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 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 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 FileReaders - * 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/ -- Building in src/utils/bedFile - * compiling bedFile.cpp -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/ - * 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 Records - * 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 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 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 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/ In file included from /usr/include/c++/8/vector:69, from ../../utils//lineFileUtilities/lineFileUtilities.h:4, from bedFile.h:17, @@ -663,8 +667,12 @@ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ - * 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 FileRecordMgr.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/ + * 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 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/ In file included from /usr/include/c++/8/vector:64, from ../../utils//lineFileUtilities/lineFileUtilities.h:4, from bedFile.h:17, @@ -673,8 +681,6 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ - * 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/ In file included from /usr/include/c++/8/algorithm:62, from bedFile.h:29, from bedFile.cpp:12: @@ -699,8 +705,10 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - * 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 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 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/ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from bedFile.h:29, @@ -709,6 +717,8 @@ /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ + * 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/ /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, @@ -745,8 +755,8 @@ /usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__make_heap(__first, __middle, __comp); ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - * 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 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/ /usr/include/c++/8/bits/stl_algo.h: In member function 'void BedFile::assignWeightsBasedOnSize()': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, @@ -779,8 +789,14 @@ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - * 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/ +- Building in FileReaders + * 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/ +- Building in src/utils/BinTree + * compiling BinTree.cpp +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 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/ In file included from /usr/include/c++/8/vector:64, from ../../utils//lineFileUtilities/lineFileUtilities.h:4, from bedFile.h:17, @@ -796,44 +812,35 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ - * 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/ - * 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 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/BinTree - * compiling BinTree.cpp -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 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 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 Records + * 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 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/ - Building in src/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 - Building in src/utils/bedGraphFile * 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/ - * 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/ - * 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 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/ - Building in src/utils/chromsweep * 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/ - * 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 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 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 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 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/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 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 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 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 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/ In file included from /usr/include/c++/8/vector:69, from ../../utils//lineFileUtilities/lineFileUtilities.h:4, from chromsweep.cpp:12: @@ -848,61 +855,85 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ + * 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/ /usr/include/c++/8/bits/stl_vector.h: In member function 'bool ChromSweep::Next(std::pair >&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -- 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 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 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 RecordKeyList.cpp -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 RecordKeyList.cpp -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/ - * 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/ + * 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/ + * 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 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/ - 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/ -- 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 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 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/ - * 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 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 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 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 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 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/ + * compiling ContextMap.cpp +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 CommonHelp.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/ + * 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/ + * 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 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 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/ +- 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 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 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/ - 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 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 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 - * 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 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 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/ 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 'unsigned int'} [-Wsign-compare] for (int j=0; j < len; j++) { ~~^~~~~ - * compiling CommonHelp.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/ - * 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 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 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/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 ContextMap.cpp -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/ -- 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 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 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 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/ In file included from /usr/include/c++/8/vector:69, from bedFilePE.h:4, from bedFilePE.cpp:15: @@ -910,8 +941,10 @@ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ - * 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 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 RecordKeyList.cpp +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/ In file included from /usr/include/c++/8/vector:64, from bedFilePE.h:4, from bedFilePE.cpp:15: @@ -928,6 +961,10 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ + * 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 RecordKeyList.cpp +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/ /usr/include/c++/8/bits/stl_vector.h: In member function 'void BedFilePE::loadBedPEFileIntoMap()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); @@ -935,17 +972,60 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ - * 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 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/ + * 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/ + * 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/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/ - Building in src/utils/NewChromsweep * 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/ +- 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 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/ +- Building in src/utils/tabFile + * 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/ +- 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 +- 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 + * 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/ +In file included from /usr/include/c++/8/vector:69, + from ..//lineFileUtilities/lineFileUtilities.h:4, + from ..//bedFile/bedFile.h:17, + from BamAncillary.h:12, + from BamAncillary.cpp:12: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ + * compiling BamMultiReader.cpp +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 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 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/ - * 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 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 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 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/BlockedIntervals + * 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 In file included from /usr/include/c++/8/algorithm:62, from ../../utils//fileType/FileRecordTypeChecker.h:18, from ../../utils//FileRecordTools/Records/Record.h:14, @@ -960,8 +1040,8 @@ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - * 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/ + * 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 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../../utils//fileType/FileRecordTypeChecker.h:18, @@ -988,6 +1068,15 @@ /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + from ..//lineFileUtilities/lineFileUtilities.h:4, + from ..//bedFile/bedFile.h:17, + from BamAncillary.h:12, + from BamAncillary.cpp:12: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../../utils//fileType/FileRecordTypeChecker.h:18, @@ -1014,8 +1103,17 @@ /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - * 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/ +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + from BlockedIntervals.h:12, + from BlockedIntervals.cpp:12: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In member function 'void KeyListOpsMethods::sortArray(bool, bool)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, @@ -1043,78 +1141,21 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -- 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 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/ -- Building in src/utils/tabFile - * 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/ - * 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 - * 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 -- 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 - * 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/ -In file included from /usr/include/c++/8/vector:69, - from ..//lineFileUtilities/lineFileUtilities.h:4, - from ..//bedFile/bedFile.h:17, - from BamAncillary.h:12, - from BamAncillary.cpp:12: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ - * compiling BamMultiReader.cpp -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 -- Building in src/utils/BlockedIntervals - * 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 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 - * 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 -In file included from /usr/include/c++/8/vector:69, - from BlockedIntervals.h:12, - from BlockedIntervals.cpp:12: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ - * 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 -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - from ..//lineFileUtilities/lineFileUtilities.h:4, - from ..//bedFile/bedFile.h:17, - from BamAncillary.h:12, - from BamAncillary.cpp:12: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ + * 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 +- 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 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ + * 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 In file included from /usr/include/c++/8/vector:64, from BlockedIntervals.h:12, from BlockedIntervals.cpp:12: @@ -1128,18 +1169,9 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ - * 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 - * 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 -- 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 - 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 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 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); @@ -1148,8 +1180,8 @@ 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 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 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 In file included from /usr/include/c++/8/map:60, from Fasta.h:12, from Fasta.cpp:9: @@ -1170,32 +1202,8 @@ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/algorithm:62, - from VectorOps.h:21, - from VectorOps.cpp:15: -/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - __insertion_sort(_RandomAccessIterator __first, - ^~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/8/vector:69, - from VectorOps.h:15, - from VectorOps.cpp:15: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 -/usr/include/c++/8/bits/vector.tcc: In function '_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator*, std::vector > >; _OIter = std::back_insert_iterator >; _UnaryOperation = double (*)(const std::__cxx11::basic_string&)]': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ + * 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 In file included from /usr/include/c++/8/algorithm:62, from Fasta.h:18, from Fasta.cpp:9: @@ -1220,8 +1228,9 @@ /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ - * 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 +- 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/ In file included from /usr/include/c++/8/algorithm:62, from Fasta.h:18, from Fasta.cpp:9: @@ -1233,6 +1242,66 @@ /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/algorithm:62, + from VectorOps.h:21, + from VectorOps.cpp:15: +/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + __insertion_sort(_RandomAccessIterator __first, + ^~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/8/map:61, + from Fasta.h:12, + from Fasta.cpp:9: +/usr/include/c++/8/bits/stl_map.h: In function 'std::ostream& operator<<(std::ostream&, FastaIndex&)': +/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, FastaIndexEntry>, std::_Select1st, FastaIndexEntry> >, std::less >, std::allocator, FastaIndexEntry> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, FastaIndexEntry> >'} changed in GCC 7.1 + __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +In file included from /usr/include/c++/8/vector:64, + from Fasta.h:15, + from Fasta.cpp:9: +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/algorithm:62, + from Fasta.h:18, + from Fasta.cpp:9: +/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + std::__introsort_loop(__first, __last, + ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + std::__lg(__last - __first) * 2, + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __comp); + ~~~~~~~ +/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + std::__insertion_sort(__first, __last, __comp); + ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + from VectorOps.h:15, + from VectorOps.cpp:15: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 +/usr/include/c++/8/bits/vector.tcc: In function '_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator*, std::vector > >; _OIter = std::back_insert_iterator >; _UnaryOperation = double (*)(const std::__cxx11::basic_string&)]': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +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 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 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from VectorOps.h:21, @@ -1267,34 +1336,8 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/map:61, - from Fasta.h:12, - from Fasta.cpp:9: -/usr/include/c++/8/bits/stl_map.h: In function 'std::ostream& operator<<(std::ostream&, FastaIndex&)': -/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, FastaIndexEntry>, std::_Select1st, FastaIndexEntry> >, std::less >, std::allocator, FastaIndexEntry> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, FastaIndexEntry> >'} changed in GCC 7.1 - __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, -In file included from /usr/include/c++/8/vector:64, - from Fasta.h:15, - from Fasta.cpp:9: -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/algorithm:62, - from Fasta.h:18, - from Fasta.cpp:9: -/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - std::__introsort_loop(__first, __last, - ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - std::__lg(__last - __first) * 2, - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __comp); - ~~~~~~~ -/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - std::__insertion_sort(__first, __last, __comp); - ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ + * 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 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from VectorOps.h:21, @@ -1362,84 +1405,108 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - * 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 - * 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/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/ + * 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/ - 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 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 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 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 - 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/ + * 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 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; ^~~~~~~~~~ -- 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/ - * 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/ - * 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 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; ^~~~~~~~~~~~~~~~~ - * 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/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 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/ 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; ^~~~~~~~~~ * 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/ - * 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 - Building in src/bedToBam * 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/ -- Building in src/bedpeToBam - * 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/ 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 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 +- Building in src/bedpeToBam + * 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/ +- 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/ + * 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 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; ^~~~~~~~~~~ +- 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/ + * 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/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 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/ +- 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 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 +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/ + * 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/ + * 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/ + * 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 +- 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/ +- 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 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 -- 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/ +- Building in src/fastaFromBed + * 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/ + * 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/ In file included from /usr/include/c++/8/vector:69, from src/api/BamAux.h:18, from src/api/BamAlignment.h:14, @@ -1466,6 +1533,8 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ + * 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/ In file included from /usr/include/c++/8/vector:69, from src/api/BamAux.h:18, from src/api/BamAlignment.h:14, @@ -1474,6 +1543,10 @@ /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ +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); + ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from src/api/BamAux.h:18, from src/api/BamAlignment.h:14, @@ -1482,6 +1555,14 @@ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ +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); + ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from src/api/BamAux.h:18, from src/api/BamAlignment.h:14, @@ -1490,9 +1571,10 @@ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ -- 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/ +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); + ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void BamTools::Internal::BamStandardIndex::CalculateCandidateOffsets(const BamTools::Internal::BaiReferenceSummary&, const uint64_t&, std::set&, std::vector&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -1539,6 +1621,9 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +- 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/ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from src/api/internal/index/BamStandardIndex_p.cpp:21: @@ -1571,16 +1656,20 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -- 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/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 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/ * 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 -- Building in src/clusterBed - * 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 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/ + * 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/ +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; + ^~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from src/api/BamAux.h:18, from src/api/BamAlignment.h:14, @@ -1595,10 +1684,6 @@ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ -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; - ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from src/api/BamAux.h:18, from src/api/BamAlignment.h:14, @@ -1607,8 +1692,6 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ - * 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/ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual bool BamTools::Internal::BamToolsIndex::Create()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); @@ -1619,161 +1702,75 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -- 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 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 - * 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/ - * 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 -- 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 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 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/ -- 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/ -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 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/fastaFromBed - * 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/ - * 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 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/ - * 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 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/ -- 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/ - * 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 - * 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 -- Building in src/getOverlap - * 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/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) | - ^~ -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 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/ - 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 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/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/ 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 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 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 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/ + * 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 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 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 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 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/ +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/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 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 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/ - * 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 -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(); - ^~~~~~~~~~~ - * 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 - 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/ - * 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 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 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/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 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 + * 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/ + * 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 + * 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/ + * 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/ - 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 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/ - * 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/ - * 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 + * 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 - 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 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/ + * 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 - 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/ + * 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/ + * 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/ + * 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/ - 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/ - * 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 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 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 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; @@ -1784,19 +1781,31 @@ multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ - * 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/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/ - * 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 - * 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 -ranlib lib/libbamtools.a + * 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 +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) | + ^~ - 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 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/ 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; @@ -1807,22 +1816,24 @@ multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] bool haveFiller = true; ^~~~~~~~~~ + * 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 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 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/ + * 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 - 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/ 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; ^~~~~~~~~~~~ -- 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/ - * 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/ 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; @@ -1830,16 +1841,14 @@ - 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/ -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; - ^~~~~~~~~~ + * 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 + * 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/ * 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 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 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; @@ -1847,8 +1856,18 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable] bool found2 = false; ^~~~~~ +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; + ^~~~~~~~~~ * 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/ + * 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 In file included from /usr/include/c++/8/vector:69, from ../utils//lineFileUtilities/lineFileUtilities.h:4, from pairToPair.cpp:12: @@ -1859,13 +1878,6 @@ - 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 -In file included from /usr/include/c++/8/vector:69, - from ../utils//lineFileUtilities/lineFileUtilities.h:4, - from pairToBed.cpp:12: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../utils//lineFileUtilities/lineFileUtilities.h:4, from pairToPair.cpp:12: @@ -1876,16 +1888,8 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - from ../utils//lineFileUtilities/lineFileUtilities.h:4, - from pairToBed.cpp:12: -/usr/include/c++/8/bits/stl_vector.h: In member function 'void BedIntersectPE::FindOverlaps(const BEDPE&, std::vector&, std::vector&, const string&)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ + * 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 /usr/include/c++/8/bits/stl_vector.h: In member function 'void PairToPair::FindHitsOnEitherEnd(const BEDPE&, const std::vector&, const std::vector&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); @@ -1893,6 +1897,13 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + from ../utils//lineFileUtilities/lineFileUtilities.h:4, + from pairToBed.cpp:12: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ 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()); @@ -1905,21 +1916,34 @@ 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 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 +In file included from /usr/include/c++/8/vector:64, + from ../utils//lineFileUtilities/lineFileUtilities.h:4, + from pairToBed.cpp:12: +/usr/include/c++/8/bits/stl_vector.h: In member function 'void BedIntersectPE::FindOverlaps(const BEDPE&, std::vector&, std::vector&, const string&)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ - 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 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 + * 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/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/ - * 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 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/ 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 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/ + * 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 + * 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/ reldist.cpp: In member function 'void RelativeDistance::ReportDistanceSummary()': reldist.cpp:69:16: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'unsigned int' [-Wformat=] printf("%.2f\t%lu\t%lu\t%.3f\n", @@ -1928,21 +1952,26 @@ freqItr->second, ~~~~~~~~~~~~~~~ reldist.cpp:69:16: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] +- 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/ - Building in src/shuffleBed * 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/ - Building in src/slopBed * 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/ + * 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 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/ + * compiling slopBed.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/ * 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/ - 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 slopBed.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/ slopBed.cpp: In member function 'void BedSlop::AddSlop(BED&)': slopBed.cpp:81:53: warning: comparison of integer expressions of different signedness: 'long int' and 'CHRPOS' {aka 'unsigned int'} [-Wsign-compare] if (((int)bed.start - (long)_rightSlop) >= chromSize && _rightSlop < 0) { @@ -1956,26 +1985,50 @@ slopBed.cpp:120:48: warning: comparison of integer expressions of different signedness: 'long int' and 'CHRPOS' {aka 'unsigned int'} [-Wsign-compare] if ( ((int)bed.end + (long)_rightSlop) <= chromSize ) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ - * 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/ + * 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 + * 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/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 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/ +ranlib lib/libbamtools.a + * 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/ - 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/ + * 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/ - 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/ In file included from /usr/include/c++/8/vector:69, from ../utils//lineFileUtilities/lineFileUtilities.h:4, + from splitBed.cpp:16: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + from ../utils//lineFileUtilities/lineFileUtilities.h:4, + from splitBed.cpp:16: +/usr/include/c++/8/bits/stl_vector.h: In member function 'void BedSplit::loadBed()': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + from ../utils//lineFileUtilities/lineFileUtilities.h:4, from sortBed.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ + * 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/ +- Building in src/tagBam + * compiling tagBamMain.cpp +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/ In file included from /usr/include/c++/8/algorithm:62, from ../utils//bedFile/bedFile.h:29, from sortBed.h:12, @@ -1984,8 +2037,19 @@ /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ - * 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/ +In file included from /usr/include/c++/8/algorithm:62, + from ../utils//bedFile/bedFile.h:29, + from splitBed.h:10, + from splitBed.cpp:18: +/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': +/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + __unguarded_linear_insert(_RandomAccessIterator __last, + ^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + __insertion_sort(_RandomAccessIterator __first, + ^~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, @@ -2006,48 +2070,72 @@ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from ../utils//bedFile/bedFile.h:29, + from splitBed.h:10, + from splitBed.cpp:18: +/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = BED; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + ^~~~~~~~~~~~~ +In file included from /usr/include/c++/8/bits/stl_algo.h:61, + from /usr/include/c++/8/algorithm:62, + from ../utils//bedFile/bedFile.h:29, from sortBed.h:12, from sortBed.cpp:14: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = BED; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - from ../utils//lineFileUtilities/lineFileUtilities.h:4, - from splitBed.cpp:16: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~~~ /usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, + ^~~~~~~~~~~ +/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + * 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/ +/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, + ^~~~~~~~~~ +/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~~ /usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/8/vector:64, - from ../utils//lineFileUtilities/lineFileUtilities.h:4, - from splitBed.cpp:16: -/usr/include/c++/8/bits/stl_vector.h: In member function 'void BedSplit::loadBed()': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../utils//bedFile/bedFile.h:29, from splitBed.h:10, from splitBed.cpp:18: -/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': -/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - __unguarded_linear_insert(_RandomAccessIterator __last, - ^~~~~~~~~~~~~~~~~~~~~~~~~ -- Building in src/tagBam - * compiling tagBamMain.cpp -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/ +/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + __introsort_loop(_RandomAccessIterator __first, + ^~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/8/bits/stl_algo.h:61, + from /usr/include/c++/8/algorithm:62, + from ../utils//bedFile/bedFile.h:29, + from splitBed.h:10, + from splitBed.cpp:18: +/usr/include/c++/8/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + std::__pop_heap(__first, __last, __last, __comp); + ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/algorithm:62, + from ../utils//bedFile/bedFile.h:29, + from splitBed.h:10, + from splitBed.cpp:18: +/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + std::__introsort_loop(__cut, __last, __depth_limit, __comp); + ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + std::__make_heap(__first, __middle, __comp); + ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from ../utils//bedFile/bedFile.h:29, from sortBed.h:12, @@ -2075,31 +2163,19 @@ /usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__make_heap(__first, __middle, __comp); ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - __insertion_sort(_RandomAccessIterator __first, - ^~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/8/bits/stl_algo.h:61, - from /usr/include/c++/8/algorithm:62, - from ../utils//bedFile/bedFile.h:29, - from splitBed.h:10, - from splitBed.cpp:18: -/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = BED; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - ^~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, - ^~~~~~~~~~~ -/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, - ^~~~~~~~~~ -/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +- Building in src/unionBedGraphs + * 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/ +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; + ^~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../utils//lineFileUtilities/lineFileUtilities.h:4, from sortBed.cpp:13: @@ -2121,33 +2197,23 @@ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/algorithm:62, - from ../utils//bedFile/bedFile.h:29, - from splitBed.h:10, - from splitBed.cpp:18: -/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - __introsort_loop(_RandomAccessIterator __first, - ^~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/8/bits/stl_algo.h:61, - from /usr/include/c++/8/algorithm:62, - from ../utils//bedFile/bedFile.h:29, - from splitBed.h:10, - from splitBed.cpp:18: -/usr/include/c++/8/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - std::__pop_heap(__first, __last, __last, __comp); - ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/algorithm:62, - from ../utils//bedFile/bedFile.h:29, - from splitBed.h:10, - from splitBed.cpp:18: -/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - std::__introsort_loop(__cut, __last, __depth_limit, __comp); - ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - std::__make_heap(__first, __middle, __comp); - ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_algo.h: In member function 'int BedSplit::doEuristicSplitOnTotalSize()': +/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + std::__introsort_loop(__first, __last, + ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + std::__lg(__last - __first) * 2, + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __comp); + ~~~~~~~ +/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + std::__insertion_sort(__first, __last, __comp); + ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +- 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/ /usr/include/c++/8/bits/stl_algo.h: In member function 'void BedSort::SortBedByChromThenSizeDesc()': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, @@ -2170,8 +2236,8 @@ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - * 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 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/ /usr/include/c++/8/bits/stl_algo.h: In member function 'void BedSort::SortBedByChromThenScoreAsc()': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, @@ -2215,40 +2281,8 @@ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_algo.h: In member function 'int BedSplit::doEuristicSplitOnTotalSize()': -/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - std::__introsort_loop(__first, __last, - ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - std::__lg(__last - __first) * 2, - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __comp); - ~~~~~~~ -/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - std::__insertion_sort(__first, __last, __comp); - ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -- Building in src/unionBedGraphs - * 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/ -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; - ^~~~~~~~~~ -- 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/ * 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/ - * 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 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/ @@ -2265,7 +2299,7 @@ make[1]: Entering directory '/build/bedtools-2.27.1+dfsg' mv test/shuffle debian/ dh_auto_test - make -j3 test + make -j4 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: @@ -2275,147 +2309,147 @@ CURRENT_VERSION = v2.27.1 - Building in src/utils/FileRecordTools - Building in src/utils/FileRecordTools/FileReaders -- Building in src/utils/FileRecordTools/Records -make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in FileReaders +- Building in src/utils/FileRecordTools/Records +- Building in Records - Building in src/utils/bedFile -- Building in src/utils/BinTree make[4]: Nothing to be done for 'all'. -- Building in Records make[4]: Nothing to be done for 'all'. +make[3]: Nothing to be done for 'all'. +- Building in src/utils/BinTree +- Building in src/utils/version make[3]: '../../../obj//bedFile.o' is up to date. make[3]: '../../../obj//BinTree.o' is up to date. -- Building in src/utils/version +make[3]: Nothing to be done for 'all'. - Building in src/utils/bedGraphFile - Building in src/utils/chromsweep -make[3]: Nothing to be done for 'all'. make[3]: '../../../obj//bedGraphFile.o' is up to date. -- Building in src/utils/Contexts make[3]: '../../../obj//chromsweep.o' is up to date. +- Building in src/utils/Contexts - Building in src/utils/general -- Building in src/utils/gzstream make[3]: Nothing to be done for 'all'. -- Building in src/utils/fileType make[3]: Nothing to be done for 'all'. +- Building in src/utils/gzstream +- Building in src/utils/fileType make[3]: '../../../obj//gzstream.o' is up to date. - Building in src/utils/bedFilePE -- Building in src/utils/KeyListOps 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. +- Building in src/utils/sequenceUtilities make[3]: Nothing to be done for 'all'. +- Building in src/utils/tabFile make[3]: Nothing to be done for 'all'. -- Building in src/utils/sequenceUtilities make[3]: '../../../obj//sequenceUtils.o' is up to date. - Building in src/utils/BamTools -- Building in src/utils/tabFile +make[3]: '../../../obj//tabFile.o' is up to date. - Building in src/utils/BamTools-Ancillary +- Building in src/utils/BlockedIntervals +make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. -make[3]: '../../../obj//tabFile.o' is up to date. make[3]: Nothing to be done for 'all'. -- Building in src/utils/BlockedIntervals - Building in src/utils/Fasta - Building in src/utils/VectorOps -make[3]: Nothing to be done for 'all'. -make[3]: Nothing to be done for 'all'. - Building in src/utils/GenomeFile +make[3]: Nothing to be done for 'all'. make[3]: '../../../obj//VectorOps.o' is up to date. - Building in src/utils/RecordOutputMgr -- Building in src/utils/ToolBase make[3]: '../../../obj//NewGenomeFile.o' is up to date. +- Building in src/utils/ToolBase make[3]: '../../../obj//RecordOutputMgr.o' is up to date. - Building in src/utils/driver make[3]: '../../../obj//ToolBase.o' is up to date. - Building in src/annotateBed +make[3]: Nothing to be done for 'all'. - Building in src/bamToBed make[3]: Nothing to be done for 'all'. - Building in src/bamToFastq make[3]: Nothing to be done for 'all'. -make[3]: Nothing to be done for 'all'. -- Building in src/bedpeToBam - Building in src/bedToBam -make[3]: Nothing to be done for 'all'. +- Building in src/bedpeToBam make[3]: Nothing to be done for 'all'. - Building in src/bedToIgv make[3]: Nothing to be done for 'all'. -- Building in src/bed12ToBed6 make[3]: Nothing to be done for 'all'. +make[3]: Nothing to be done for 'all'. +- Building in src/bed12ToBed6 - Building in src/closestFile +make[3]: Nothing to be done for 'all'. - Building in src/clusterBed make[3]: Nothing to be done for 'all'. - Building in src/complementFile make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/coverageFile -make[3]: Nothing to be done for 'all'. - Building in src/expand - Building in src/fastaFromBed make[3]: Nothing to be done for 'all'. -- Building in src/flankBed make[3]: Nothing to be done for 'all'. +- Building in src/flankBed make[3]: Nothing to be done for 'all'. - Building in src/genomeCoverageBed -- Building in src/getOverlap make[3]: Nothing to be done for 'all'. 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/intersectFile - Building in src/fisher -- Building in src/groupBy -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/jaccard - Building in src/linksBed -- Building in src/maskFastaFromBed make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. +- Building in src/maskFastaFromBed - Building in src/mapFile make[3]: Nothing to be done for 'all'. +make[3]: Nothing to be done for 'all'. - Building in src/mergeFile - Building in src/multiBamCov make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/multiIntersectBed -make[3]: Nothing to be done for 'all'. - Building in src/nucBed make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/pairToBed - Building in src/pairToPair -- Building in src/randomBed 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 make[3]: Nothing to be done for 'all'. +- 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 - Building in src/shiftBed -make[3]: Nothing to be done for 'all'. +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/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'. make[3]: Nothing to be done for 'all'. - Building in src/sortBed +make[3]: Nothing to be done for 'all'. - Building in src/spacingFile +- Building in src/split make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. -- Building in src/split - Building in src/subtractFile make[3]: Nothing to be done for 'all'. -make[3]: Nothing to be done for 'all'. - Building in src/tagBam - Building in src/unionBedGraphs make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/windowBed -- Building in src/windowMaker make[3]: Nothing to be done for 'all'. +- Building in src/windowMaker 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] @@ -3265,7 +3299,7 @@ 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 -j3 install DESTDIR=/build/bedtools-2.27.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + make -j4 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: @@ -3276,76 +3310,75 @@ - Building in src/utils/FileRecordTools - Building in src/utils/FileRecordTools/FileReaders - Building in src/utils/FileRecordTools/Records +- Building in src/utils/bedFile make[2]: Nothing to be done for 'all'. - Building in FileReaders +make[2]: '../../../obj//bedFile.o' is up to date. make[2]: Nothing to be done for 'all'. -- Building in src/utils/bedFile +- Building in src/utils/BinTree +- Building in src/utils/version - Building in Records make[3]: Nothing to be done for 'all'. -- Building in src/utils/BinTree -make[2]: '../../../obj//bedFile.o' is up to date. make[3]: Nothing to be done for 'all'. -- Building in src/utils/version -- Building in src/utils/bedGraphFile make[2]: '../../../obj//BinTree.o' is up to date. -- Building in src/utils/chromsweep -make[2]: '../../../obj//bedGraphFile.o' is up to date. +- Building in src/utils/bedGraphFile make[2]: Nothing to be done for 'all'. +- Building in src/utils/chromsweep - Building in src/utils/Contexts -make[2]: '../../../obj//chromsweep.o' is up to date. - Building in src/utils/general -- Building in src/utils/gzstream +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]: Nothing to be done for 'all'. -make[2]: '../../../obj//gzstream.o' is up to date. +- Building in src/utils/gzstream - Building in src/utils/fileType -- Building in src/utils/bedFilePE - Building in src/utils/KeyListOps +- Building in src/utils/bedFilePE make[2]: Nothing to be done for 'all'. -make[2]: '../../../obj//bedFilePE.o' is up to date. +make[2]: '../../../obj//gzstream.o' is up to date. - Building in src/utils/NewChromsweep -make[2]: Nothing to be done for 'all'. - Building in src/utils/sequenceUtilities -- Building in src/utils/tabFile +make[2]: '../../../obj//bedFilePE.o' is up to date. make[2]: Nothing to be done for 'all'. +- Building in src/utils/tabFile make[2]: '../../../obj//sequenceUtils.o' is up to date. - Building in src/utils/BamTools -make[2]: '../../../obj//tabFile.o' is up to date. - Building in src/utils/BamTools-Ancillary -- Building in src/utils/BlockedIntervals +make[2]: '../../../obj//tabFile.o' is up to date. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. +- Building in src/utils/BlockedIntervals +make[2]: Nothing to be done for 'all'. - Building in src/utils/Fasta -- Building in src/utils/VectorOps make[2]: Nothing to be done for 'all'. +- Building in src/utils/VectorOps - Building in src/utils/GenomeFile +- Building in src/utils/RecordOutputMgr make[2]: Nothing to be done for 'all'. make[2]: '../../../obj//VectorOps.o' is up to date. -- Building in src/utils/RecordOutputMgr -- Building in src/utils/ToolBase make[2]: '../../../obj//NewGenomeFile.o' is up to date. -make[2]: '../../../obj//RecordOutputMgr.o' is up to date. +- Building in src/utils/ToolBase - Building in src/utils/driver -make[2]: '../../../obj//ToolBase.o' is up to date. +make[2]: '../../../obj//RecordOutputMgr.o' is up to date. - Building in src/annotateBed - Building in src/bamToBed -make[2]: Nothing to be done for 'all'. -make[2]: Nothing to be done for 'all'. +make[2]: '../../../obj//ToolBase.o' is up to date. make[2]: Nothing to be done for 'all'. - Building in src/bamToFastq - Building in src/bedToBam -- Building in src/bedpeToBam make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. -- Building in src/bedToIgv -- Building in src/bed12ToBed6 make[2]: Nothing to be done for 'all'. +- Building in src/bedpeToBam +- Building in src/bedToIgv make[2]: Nothing to be done for 'all'. +- Building in src/bed12ToBed6 - Building in src/closestFile make[2]: Nothing to be done for 'all'. +make[2]: Nothing to be done for 'all'. - Building in src/clusterBed -- Building in src/complementFile make[2]: Nothing to be done for 'all'. +- Building in src/complementFile - Building in src/coverageFile make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. @@ -3356,27 +3389,28 @@ - Building in src/flankBed - Building in src/genomeCoverageBed make[2]: Nothing to be done for 'all'. +make[2]: Nothing to be done for 'all'. - Building in src/getOverlap +- Building in src/groupBy make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. -- Building in src/groupBy - Building in src/intersectFile -make[2]: Nothing to be done for 'all'. - 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'. - Building in src/jaccard - Building in src/linksBed make[2]: Nothing to be done for 'all'. - Building in src/maskFastaFromBed +- Building in src/mapFile +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/mapFile make[2]: Nothing to be done for 'all'. - Building in src/mergeFile - Building in src/multiBamCov 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'. - Building in src/nucBed @@ -3384,37 +3418,37 @@ make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in src/pairToPair -make[2]: Nothing to be done for 'all'. - Building in src/randomBed - Building in src/regressTest make[2]: Nothing to be done for 'all'. -- Building in src/reldist make[2]: Nothing to be done for 'all'. -- Building in src/sampleFile +make[2]: Nothing to be done for 'all'. +- Building in src/reldist compiling RegressTest.cpp +- Building in src/sampleFile 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[2]: Nothing to be done for 'all'. - Building in src/shiftBed make[2]: Nothing to be done for 'all'. -- Building in src/shuffleBed -make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. +- Building in src/shuffleBed - Building in src/slopBed +make[2]: Nothing to be done for 'all'. - Building in src/sortBed make[2]: Nothing to be done for 'all'. -- Building in src/spacingFile make[2]: Nothing to be done for 'all'. +- Building in src/spacingFile - Building in src/split make[2]: Nothing to be done for 'all'. -make[2]: Nothing to be done for 'all'. - Building in src/subtractFile -- Building in src/tagBam make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. +- Building in src/tagBam - Building in src/unionBedGraphs +make[2]: Nothing to be done for 'all'. - Building in src/windowBed 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/windowMaker make[2]: Nothing to be done for 'all'. RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)': @@ -3481,30 +3515,30 @@ 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-test/usr/share/doc/bedtools-test/changelog.Debian - install -p -m0644 RELEASE_HISTORY debian/bedtools-test/usr/share/doc/bedtools-test/changelog 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/test/intersect/a_bgzipped.bed.gz using File::StripNondeterminism::handlers::gzip + Normalizing debian/bedtools-test/usr/share/bedtools/data/aluY.chr1.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/test/general/non-empty.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/bug44_a.vcf.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/test/intersect/a_withLargeHeader_gzipped.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/test/intersect/a_gzipped.bed.gz using File::StripNondeterminism::handlers::gzip - Normalizing debian/bedtools-test/usr/share/bedtools/data/simpleRepeats.chr1.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/data/gerp.chr1.bed.gz using File::StripNondeterminism::handlers::gzip + Normalizing debian/bedtools-test/usr/share/bedtools/data/simpleRepeats.chr1.bed.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/bedtools-test/usr/share/bedtools/data/refseq.chr1.exons.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/changelog usr/share/doc/bedtools/changelog.Debian 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' @@ -3556,30 +3590,30 @@ 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=de4bacfd9d541c9cd8d8ef137432c8ab4f54bcaf -DSection=debug -UMulti-Arch -UReplaces -UBreaks + chmod 0644 -- debian/bedtools-test/DEBIAN/control + chown 0:0 -- debian/bedtools-test/DEBIAN/control 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/bedtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/bedtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/bedtools-test/DEBIAN/md5sums chown 0:0 -- debian/bedtools-test/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_armhf.deb'. -dpkg-deb: building package 'bedtools-test' in '../bedtools-test_2.27.1+dfsg-4_all.deb'. + dpkg-deb --build debian/bedtools-test .. + dpkg-deb --build debian/bedtools .. dpkg-deb: building package 'bedtools' in '../bedtools_2.27.1+dfsg-4_armhf.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_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3587,12 +3621,14 @@ 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/26160/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/26160/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/13845 and its subdirectories -I: Current time: Sun Aug 9 20:58:07 -12 2020 -I: pbuilder-time-stamp: 1597049887 +I: removing directory /srv/workspace/pbuilder/26160 and its subdirectories +I: Current time: Mon Aug 10 23:10:58 +14 2020 +I: pbuilder-time-stamp: 1597050658