https://launchpad.net/ubuntu/+source/bedtools/2.27.1+dfsg-3/+build/16364536 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lcy01-amd64-026 4.4.0-142-generic #168-Ubuntu SMP Wed Jan 16 21:00:45 UTC 2019 x86_64 Buildd toolchain package versions: launchpad-buildd_166 python-lpbuildd_166 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 7 Feb 17:11:34 ntpdate[1793]: adjust time server 10.211.37.1 offset 0.019317 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-16364536 /home/buildd/filecache-default/1b8bd95dfc080fb8062b439d66609df4d6cce84f Creating target for build PACKAGEBUILD-16364536 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-16364536 Starting target for build PACKAGEBUILD-16364536 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-16364536 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-16364536 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-16364536 Updating target for build PACKAGEBUILD-16364536 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main i386 Packages [977 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [508 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe i386 Packages [9004 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5258 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main i386 Packages [63.9 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [24.6 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe i386 Packages [213 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [107 kB] Fetched 16.6 MB in 5s (3260 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libreadline7 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: gcc-9-base libreadline8 The following packages will be upgraded: adduser apt bash binutils binutils-common binutils-i686-linux-gnu bsdutils ca-certificates coreutils cpp-8 dash debconf debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk findutils g++-8 gcc-8 gcc-8-base gpg gpg-agent gpgconf gpgv grep gzip init init-system-helpers libapt-pkg5.0 libargon2-1 libasan5 libassuan0 libatomic1 libbinutils libblkid1 libcap-ng0 libcap2 libcc1-0 libcom-err2 libcomerr2 libcryptsetup12 libdb5.3 libdebconfclient0 libdpkg-perl libext2fs2 libfdisk1 libgcc-8-dev libgcc1 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libhogweed4 libip4tc0 libitm1 libjson-c3 liblz4-1 liblzma5 libmount1 libmpfr6 libmpx2 libnettle6 libperl5.28 libpng16-16 libquadmath0 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 libstdc++-8-dev libstdc++6 libsystemd0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login lsb-base mount passwd perl perl-base perl-modules-5.28 pkgbinarymangler readline-common sed systemd systemd-sysv tar tzdata util-linux xz-utils zlib1g 98 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 66.9 MB of archives. After this operation, 7737 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main i386 debianutils i386 4.8.6.1 [85.9 kB] Get:2 http://ftpmaster.internal/ubuntu disco/main i386 bash i386 5.0-2ubuntu1 [677 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main i386 bsdutils i386 1:2.33.1-0.1ubuntu1 [65.9 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main i386 coreutils i386 8.30-1ubuntu1 [1316 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main i386 tar i386 1.30+dfsg-5 [265 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main i386 dpkg i386 1.19.2ubuntu2 [1124 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main i386 libperl5.28 i386 5.28.1-4 [3445 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main i386 perl i386 5.28.1-4 [204 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main i386 perl-base i386 5.28.1-4 [1602 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main i386 perl-modules-5.28 all 5.28.1-4 [2811 kB] Get:11 http://ftpmaster.internal/ubuntu disco/main i386 libdb5.3 i386 5.3.28+dfsg1-0.3 [737 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main i386 libgdbm6 i386 1.18.1-2build1 [32.0 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main i386 libgdbm-compat4 i386 1.18.1-2build1 [6708 B] Get:14 http://ftpmaster.internal/ubuntu disco/main i386 zlib1g i386 1:1.2.11.dfsg-1ubuntu2 [55.9 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main i386 debconf all 1.5.70 [122 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main i386 dash i386 0.5.10.2-4ubuntu1 [90.8 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main i386 findutils i386 4.6.0+git+20190105-2 [343 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main i386 grep i386 3.3-1 [155 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main i386 gzip i386 1.9-3 [94.8 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main i386 libsmartcols1 i386 2.33.1-0.1ubuntu1 [98.7 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main i386 libuuid1 i386 2.33.1-0.1ubuntu1 [21.9 kB] Get:22 http://ftpmaster.internal/ubuntu disco/main i386 libblkid1 i386 2.33.1-0.1ubuntu1 [147 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main i386 libfdisk1 i386 2.33.1-0.1ubuntu1 [190 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main i386 libmount1 i386 2.33.1-0.1ubuntu1 [158 kB] Get:25 http://ftpmaster.internal/ubuntu disco/main i386 fdisk i386 2.33.1-0.1ubuntu1 [126 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main i386 login i386 1:4.5-1.1ubuntu1 [266 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main i386 util-linux i386 2.33.1-0.1ubuntu1 [1026 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main i386 sed i386 4.7-1 [193 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main i386 init-system-helpers all 1.56+nmu1 [38.2 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main i386 libnettle6 i386 3.4.1-1 [128 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main i386 libhogweed4 i386 3.4.1-1 [142 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main i386 libgnutls30 i386 3.6.5-2ubuntu1 [770 kB] Get:33 http://ftpmaster.internal/ubuntu disco-proposed/main i386 gcc-9-base i386 9-20190202-1ubuntu1 [17.1 kB] Get:34 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libgcc1 i386 1:9-20190202-1ubuntu1 [47.9 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main i386 liblz4-1 i386 1.8.3-1ubuntu1 [61.2 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main i386 liblzma5 i386 5.2.4-1 [99.7 kB] Get:37 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libstdc++6 i386 9-20190202-1ubuntu1 [545 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main i386 libudev1 i386 240-5ubuntu3 [73.1 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main i386 libzstd1 i386 1.3.8+dfsg-3 [225 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main i386 libapt-pkg5.0 i386 1.8.0~rc2 [897 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main i386 libsemanage-common all 2.8-2 [7016 B] Get:42 http://ftpmaster.internal/ubuntu disco/main i386 libsemanage1 i386 2.8-2 [94.2 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main i386 passwd i386 1:4.5-1.1ubuntu1 [817 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main i386 adduser all 3.118ubuntu1 [163 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main i386 libgpg-error0 i386 1.35-1 [62.3 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main i386 gpgv i386 2.2.12-1ubuntu3 [217 kB] Get:47 http://ftpmaster.internal/ubuntu disco/main i386 apt i386 1.8.0~rc2 [1198 kB] Get:48 http://ftpmaster.internal/ubuntu disco/main i386 systemd-sysv i386 240-5ubuntu3 [9380 B] Get:49 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libcap2 i386 1:2.25-2 [13.7 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main i386 libargon2-1 i386 0~20171227-0.2 [23.5 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main i386 libjson-c3 i386 0.12.1+ds-2 [24.0 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main i386 libcryptsetup12 i386 2:2.0.6-1ubuntu1 [157 kB] Get:53 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libip4tc0 i386 1.8.2-3ubuntu1 [21.5 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main i386 mount i386 2.33.1-0.1ubuntu1 [117 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main i386 systemd i386 240-5ubuntu3 [3463 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main i386 libsystemd0 i386 240-5ubuntu3 [267 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main i386 libext2fs2 i386 1.44.5-1 [186 kB] Get:58 http://ftpmaster.internal/ubuntu disco/main i386 e2fsprogs i386 1.44.5-1 [550 kB] Get:59 http://ftpmaster.internal/ubuntu disco/main i386 init i386 1.56+nmu1 [6076 B] Get:60 http://ftpmaster.internal/ubuntu disco/main i386 libcap-ng0 i386 0.7.9-2 [11.1 kB] Get:61 http://ftpmaster.internal/ubuntu disco/main i386 libdebconfclient0 i386 0.246ubuntu1 [6436 B] Get:62 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libubsan1 i386 9-20190202-1ubuntu1 [148 kB] Get:63 http://ftpmaster.internal/ubuntu disco/main i386 libmpfr6 i386 4.0.2-1 [246 kB] Get:64 http://ftpmaster.internal/ubuntu disco-proposed/main i386 g++-8 i386 8.2.0-17ubuntu6 [10.1 MB] Get:65 http://ftpmaster.internal/ubuntu disco-proposed/main i386 gcc-8 i386 8.2.0-17ubuntu6 [9841 kB] Get:66 http://ftpmaster.internal/ubuntu disco-proposed/main i386 cpp-8 i386 8.2.0-17ubuntu6 [8978 kB] Get:67 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libcc1-0 i386 9-20190202-1ubuntu1 [49.3 kB] Get:68 http://ftpmaster.internal/ubuntu disco-proposed/main i386 binutils-i686-linux-gnu i386 2.32-1ubuntu1 [2006 kB] Get:69 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libbinutils i386 2.32-1ubuntu1 [509 kB] Get:70 http://ftpmaster.internal/ubuntu disco-proposed/main i386 binutils i386 2.32-1ubuntu1 [3396 B] Get:71 http://ftpmaster.internal/ubuntu disco-proposed/main i386 binutils-common i386 2.32-1ubuntu1 [200 kB] Get:72 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libgomp1 i386 9-20190202-1ubuntu1 [94.5 kB] Get:73 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libitm1 i386 9-20190202-1ubuntu1 [30.7 kB] Get:74 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libatomic1 i386 9-20190202-1ubuntu1 [9716 B] Get:75 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libasan5 i386 9-20190202-1ubuntu1 [408 kB] Get:76 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libmpx2 i386 8.2.0-17ubuntu6 [13.0 kB] Get:77 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libquadmath0 i386 9-20190202-1ubuntu1 [230 kB] Get:78 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libstdc++-8-dev i386 8.2.0-17ubuntu6 [1569 kB] Get:79 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libgcc-8-dev i386 8.2.0-17ubuntu6 [2302 kB] Get:80 http://ftpmaster.internal/ubuntu disco-proposed/main i386 gcc-8-base i386 8.2.0-17ubuntu6 [18.9 kB] Get:81 http://ftpmaster.internal/ubuntu disco/main i386 libcom-err2 i386 1.44.5-1 [9708 B] Get:82 http://ftpmaster.internal/ubuntu disco/main i386 libss2 i386 1.44.5-1 [11.6 kB] Get:83 http://ftpmaster.internal/ubuntu disco/main i386 lsb-base all 10.2018112800ubuntu1 [12.6 kB] Get:84 http://ftpmaster.internal/ubuntu disco/main i386 ca-certificates all 20190110 [146 kB] Get:85 http://ftpmaster.internal/ubuntu disco/main i386 readline-common all 8.0-1 [53.4 kB] Get:86 http://ftpmaster.internal/ubuntu disco/main i386 libreadline8 i386 8.0-1 [133 kB] Get:87 http://ftpmaster.internal/ubuntu disco/main i386 libsqlite3-0 i386 3.26.0+fossilbc891ac6b-2 [566 kB] Get:88 http://ftpmaster.internal/ubuntu disco/main i386 tzdata all 2018i-1 [189 kB] Get:89 http://ftpmaster.internal/ubuntu disco/main i386 xz-utils i386 5.2.4-1 [87.0 kB] Get:90 http://ftpmaster.internal/ubuntu disco/main i386 libpng16-16 i386 1.6.36-5 [187 kB] Get:91 http://ftpmaster.internal/ubuntu disco/main i386 dpkg-dev all 1.19.2ubuntu2 [549 kB] Get:92 http://ftpmaster.internal/ubuntu disco/main i386 libdpkg-perl all 1.19.2ubuntu2 [227 kB] Get:93 http://ftpmaster.internal/ubuntu disco/main i386 e2fslibs i386 1.44.5-1 [2704 B] Get:94 http://ftpmaster.internal/ubuntu disco/main i386 libassuan0 i386 2.5.2-1 [37.4 kB] Get:95 http://ftpmaster.internal/ubuntu disco/main i386 gpg i386 2.2.12-1ubuntu3 [514 kB] Get:96 http://ftpmaster.internal/ubuntu disco/main i386 gpgconf i386 2.2.12-1ubuntu3 [130 kB] Get:97 http://ftpmaster.internal/ubuntu disco/main i386 gpg-agent i386 2.2.12-1ubuntu3 [249 kB] Get:98 http://ftpmaster.internal/ubuntu disco/main i386 libcomerr2 i386 1.44.5-1 [2700 B] Get:99 http://ftpmaster.internal/ubuntu disco/main i386 linux-libc-dev i386 4.19.0-12.13 [1070 kB] Get:100 http://ftpmaster.internal/ubuntu disco/main i386 pkgbinarymangler all 144 [55.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 66.9 MB in 3s (19.8 MB/s) (Reading database ... 12659 files and directories currently installed.) 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-16364536 i386 disco-proposed -c chroot:build-PACKAGEBUILD-16364536 --arch=i386 --dist=disco-proposed --nolog bedtools_2.27.1+dfsg-3.dsc Initiating build PACKAGEBUILD-16364536 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-142-generic #168-Ubuntu SMP Wed Jan 16 21:00:45 UTC 2019 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-026.buildd +==============================================================================+ | bedtools 2.27.1+dfsg-3 (i386) 07 Feb 2019 17:12 | +==============================================================================+ Package: bedtools Version: 2.27.1+dfsg-3 Source Version: 2.27.1+dfsg-3 Distribution: disco-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/bedtools-KCsLHH/bedtools-2.27.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/bedtools-KCsLHH' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-16364536/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bedtools_2.27.1+dfsg-3.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-YMcPtq/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-YMcPtq/apt_archive ./ InRelease Get:2 copy:/<>/resolver-YMcPtq/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-YMcPtq/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-YMcPtq/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-YMcPtq/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (174 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libreadline7 Use 'apt autoremove' to remove it. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-YMcPtq/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12695 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), python, zlib1g-dev, samtools Filtered Build-Depends: debhelper (>= 11~), python, zlib1g-dev, samtools dpkg-deb: building package 'sbuild-build-depends-bedtools-dummy' in '/<>/resolver-wpYhTs/apt_archive/sbuild-build-depends-bedtools-dummy.deb'. Ign:1 copy:/<>/resolver-wpYhTs/apt_archive ./ InRelease Get:2 copy:/<>/resolver-wpYhTs/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-wpYhTs/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-wpYhTs/apt_archive ./ Sources [229 B] Get:5 copy:/<>/resolver-wpYhTs/apt_archive ./ Packages [549 B] Fetched 2897 B in 0s (172 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install bedtools build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libreadline7 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libcroco3 libcurl3-gnutls libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts2 libhx509-5-heimdal libicu63 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-minimal python2 python2-minimal python2.7 python2.7-minimal samtools zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk python2-doc python2.7-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl cwltool The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libcroco3 libcurl3-gnutls libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts2 libhx509-5-heimdal libicu63 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-minimal python2 python2-minimal python2.7 python2.7-minimal samtools sbuild-build-depends-bedtools-dummy zlib1g-dev 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 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Setting up libsasl2-2:i386 (2.1.27+dfsg-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libpipeline1:i386 (1.5.1-1) ... Setting up libroken18-heimdal:i386 (7.5.0+dfsg-2.1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2) ... Setting up m4 (1.4.18-2) ... Setting up libbsd0:i386 (0.9.1-1) ... Setting up libkrb5support0:i386 (1.17-1) ... Setting up libxml2:i386 (2.9.4+dfsg1-7ubuntu3) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up libmagic-mgc (1:5.35-2) ... Setting up libmagic1:i386 (1:5.35-2) ... Setting up libcroco3:i386 (0.6.12-3) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up dwz (0.12-3) ... Setting up autotools-dev (20180224.1) ... Setting up libheimbase1-heimdal:i386 (7.5.0+dfsg-2.1) ... Setting up libkeyutils1:i386 (1.5.9-10) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libpython2.7-stdlib:i386 (2.7.15-8) ... Setting up autopoint (0.19.8.1-9) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-1ubuntu2) ... Setting up libfile-stripnondeterminism-perl (1.1.0-1) ... Setting up libk5crypto3:i386 (1.17-1) ... Setting up libwind0-heimdal:i386 (7.5.0+dfsg-2.1) ... Setting up gettext (0.19.8.1-9) ... Setting up libasn1-8-heimdal:i386 (7.5.0+dfsg-2.1) ... Setting up groff-base (1.22.4-2) ... Setting up libhcrypto4-heimdal:i386 (7.5.0+dfsg-2.1) ... Setting up python2.7 (2.7.15-8) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.35-2) ... Setting up libhx509-5-heimdal:i386 (7.5.0+dfsg-2.1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.5-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libpython2-stdlib:i386 (2.7.15-4) ... Setting up libkrb5-3:i386 (1.17-1) ... Setting up libkrb5-26-heimdal:i386 (7.5.0+dfsg-2.1) ... Setting up libheimntlm0-heimdal:i386 (7.5.0+dfsg-2.1) ... Setting up libtool (2.4.6-9) ... Setting up po-debconf (1.0.21) ... Setting up python2 (2.7.15-4) ... Setting up libgssapi-krb5-2:i386 (1.17-1) ... Setting up libpython-stdlib:i386 (2.7.15-4) ... Setting up libssh-4:i386 (0.8.6-2) ... Setting up libgssapi3-heimdal:i386 (7.5.0+dfsg-2.1) ... Setting up python (2.7.15-4) ... Setting up libldap-2.4-2:i386 (2.4.47+dfsg-2ubuntu1) ... Setting up libcurl3-gnutls:i386 (7.63.0-1ubuntu1) ... Setting up libhts2:i386 (1.9-10) ... Setting up samtools (1.9-3) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12ubuntu1) ... Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (1.1.0-1) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-142-generic amd64 (i686) Toolchain package versions: binutils_2.32-1ubuntu1 dpkg-dev_1.19.2ubuntu2 g++-8_8.2.0-17ubuntu6 gcc-8_8.2.0-17ubuntu6 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-17ubuntu6 libstdc++6_9-20190202-1ubuntu1 linux-libc-dev_4.19.0-12.13 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-1 apt_1.8.0~rc2 autoconf_2.69-11 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_5.0-2ubuntu1 binutils_2.32-1ubuntu1 binutils-common_2.32-1ubuntu1 binutils-i686-linux-gnu_2.32-1ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.33.1-0.1ubuntu1 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20190110 coreutils_8.30-1ubuntu1 cpp_4:8.2.0-2ubuntu2 cpp-8_8.2.0-17ubuntu6 dash_0.5.10.2-4ubuntu1 debconf_1.5.70 debhelper_12ubuntu1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.0-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu4 dpkg_1.19.2ubuntu2 dpkg-dev_1.19.2ubuntu2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1ubuntu1 file_1:5.35-2 findutils_4.6.0+git+20190105-2 g++_4:8.2.0-2ubuntu2 g++-8_8.2.0-17ubuntu6 gcc_4:8.2.0-2ubuntu2 gcc-8_8.2.0-17ubuntu6 gcc-8-base_8.2.0-17ubuntu6 gcc-9-base_9-20190202-1ubuntu1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpg_2.2.12-1ubuntu3 gpg-agent_2.2.12-1ubuntu3 gpgconf_2.2.12-1ubuntu3 gpgv_2.2.12-1ubuntu3 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 init_1.56+nmu1 init-system-helpers_1.56+nmu1 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.5 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu10 libapt-pkg5.0_1.8.0~rc2 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.2 libasan5_9-20190202-1ubuntu1 libasn1-8-heimdal_7.5.0+dfsg-2.1 libassuan0_2.5.2-1 libatomic1_9-20190202-1ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu3 libaudit1_1:2.8.3-1ubuntu3 libbinutils_2.32-1ubuntu1 libblkid1_2.33.1-0.1ubuntu1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-0ubuntu1 libc-dev-bin_2.28-0ubuntu1 libc6_2.28-0ubuntu1 libc6-dev_2.28-0ubuntu1 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcc1-0_9-20190202-1ubuntu1 libcom-err2_1.44.5-1 libcomerr2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.0.6-1ubuntu1 libcurl3-gnutls_7.63.0-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.3 libdebconfclient0_0.246ubuntu1 libdeflate0_1.2-1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu4 libdpkg-perl_1.19.2ubuntu2 libelf1_0.175-2 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1ubuntu1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.0-1 libgcc-8-dev_8.2.0-17ubuntu6 libgcc1_1:9-20190202-1ubuntu1 libgcrypt20_1.8.4-3ubuntu1 libgdbm-compat4_1.18.1-2build1 libgdbm6_1.18.1-2build1 libglib2.0-0_2.58.2-4 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2ubuntu1 libgomp1_9-20190202-1ubuntu1 libgpg-error0_1.35-1 libgssapi-krb5-2_1.17-1 libgssapi3-heimdal_7.5.0+dfsg-2.1 libhcrypto4-heimdal_7.5.0+dfsg-2.1 libheimbase1-heimdal_7.5.0+dfsg-2.1 libheimntlm0-heimdal_7.5.0+dfsg-2.1 libhogweed4_3.4.1-1 libhts2_1.9-10 libhx509-5-heimdal_7.5.0+dfsg-2.1 libicu63_63.1-6 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3ubuntu1 libisl19_0.20-2 libitm1_9-20190202-1ubuntu1 libjson-c3_0.12.1+ds-2 libk5crypto3_1.17-1 libkeyutils1_1.5.9-10 libkmod2_25-1ubuntu2 libkrb5-26-heimdal_7.5.0+dfsg-2.1 libkrb5-3_1.17-1 libkrb5support0_1.17-1 libldap-2.4-2_2.4.47+dfsg-2ubuntu1 libldap-common_2.4.47+dfsg-2ubuntu1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblz4-1_1.8.3-1ubuntu1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-2 libmagic1_1:5.35-2 libmount1_2.33.1-0.1ubuntu1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.2.0-17ubuntu6 libncurses6_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4.1-1 libnghttp2-14_1.36.0-2 libnpth0_1.6-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-11 libperl5.28_5.28.1-4 libpipeline1_1.5.1-1 libpng16-16_1.6.36-5 libprocps7_2:3.3.15-2ubuntu1 libpsl5_0.20.2-2 libpython-stdlib_2.7.15-4 libpython2-stdlib_2.7.15-4 libpython2.7-minimal_2.7.15-8 libpython2.7-stdlib_2.7.15-8 libquadmath0_9-20190202-1ubuntu1 libreadline7_7.0-5 libreadline8_8.0-1 libroken18-heimdal_7.5.0+dfsg-2.1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-3ubuntu2 libselinux1_2.8-1build2 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.33.1-0.1ubuntu1 libsqlite3-0_3.26.0+fossilbc891ac6b-2 libss2_1.44.5-1 libssh-4_0.8.6-2 libssl1.1_1.1.1a-1ubuntu2 libstdc++-8-dev_8.2.0-17ubuntu6 libstdc++6_9-20190202-1ubuntu1 libsystemd0_240-5ubuntu3 libtasn1-6_4.13-3 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-9 libubsan1_9-20190202-1ubuntu1 libuchardet0_0.0.6-3 libudev1_240-5ubuntu3 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.33.1-0.1ubuntu1 libwind0-heimdal_7.5.0+dfsg-2.1 libxml2_2.9.4+dfsg1-7ubuntu3 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.0-12.13 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu1 lsb-base_10.2018112800ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-1 mawk_1.3.3-17ubuntu3 mime-support_3.60ubuntu1 mount_2.33.1-0.1ubuntu1 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.1a-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1.1ubuntu1 patch_2.7.6-3 perl_5.28.1-4 perl-base_5.28.1-4 perl-modules-5.28_5.28.1-4 pinentry-curses_1.1.0-1build2 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 python_2.7.15-4 python-minimal_2.7.15-4 python2_2.7.15-4 python2-minimal_2.7.15-4 python2.7_2.7.15-8 python2.7-minimal_2.7.15-8 readline-common_8.0-1 samtools_1.9-3 sbuild-build-depends-bedtools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-5ubuntu3 systemd-sysv_240-5ubuntu3 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tar_1.30+dfsg-5 tzdata_2018i-1 ubuntu-keyring_2018.09.18.1 util-linux_2.33.1-0.1ubuntu1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu2 zlib1g-dev_1:1.2.11.dfsg-1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Feb 7 11:55:39 2019 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bedtools_2.27.1+dfsg-3.dsc dpkg-source: info: extracting bedtools in bedtools-2.27.1+dfsg dpkg-source: info: unpacking bedtools_2.27.1+dfsg.orig.tar.xz dpkg-source: info: unpacking bedtools_2.27.1+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gzstream.h.patch dpkg-source: info: applying fix_test_script.patch dpkg-source: info: applying remove_barski_binding_site.png.patch dpkg-source: info: applying reproducible_build.patch dpkg-source: info: applying louder dpkg-source: info: applying flag_no_overwrite Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-16364536 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-16364536 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-16364536 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package bedtools dpkg-buildpackage: info: source version 2.27.1+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 dpkg-source: info: using options from bedtools-2.27.1+dfsg/debian/source/options: --single-debian-patch fakeroot debian/rules clean dh clean dh_auto_clean make -j4 clean make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' * Cleaning-up BamTools API * Cleaning up. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/bedtools.substvars debian/bedtools-test.substvars debian/files rm -fr -- debian/bedtools/ debian/tmp/ debian/bedtools-test/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' $CXXFLAGS is [-g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11] Building BEDTools: ========================================================= * Creating BamTools API DETECTED_VERSION = v2.27.1 CURRENT_VERSION = Updating version file. - Building in src/utils/FileRecordTools - Building in src/utils/FileRecordTools/FileReaders - Building in src/utils/FileRecordTools/Records - Building in src/utils/bedFile * compiling FileRecordMgr.cpp g++ -c -o ../../../obj//FileRecordMgr.o FileRecordMgr.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 FileReader.cpp * compiling bedFile.cpp g++ -c -o ../../../obj//bedFile.o bedFile.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//gzstream/ -I../../utils//fileType/ -I../../utils//stringUtilities/ g++ -c -o ../../../../obj//FileReader.o FileReader.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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//Record.o Record.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 SingleLineDelimTextFileReader.cpp g++ -c -o ../../../../obj//SingleLineDelimTextFileReader.o SingleLineDelimTextFileReader.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 g++ -c -o ../../../../obj//EmptyRecord.o EmptyRecord.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 Bed3Interval.cpp g++ -c -o ../../../../obj//Bed3Interval.o Bed3Interval.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 BedGraphInterval.cpp g++ -c -o ../../../../obj//BedGraphInterval.o BedGraphInterval.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 InputStreamMgr.cpp g++ -c -o ../../../../obj//InputStreamMgr.o InputStreamMgr.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 Records * compiling Bed6Interval.cpp g++ -c -o ../../../../obj//Bed6Interval.o Bed6Interval.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 Bed6Interval.cpp g++ -c -o ../../../../obj//Bed6Interval.o Bed6Interval.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 BedPlusInterval.cpp g++ -c -o ../../../../obj//BedPlusInterval.o BedPlusInterval.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 GffPlusRecord.cpp g++ -c -o ../../../../obj//GffPlusRecord.o GffPlusRecord.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 NoPosPlusRecord.cpp g++ -c -o ../../../../obj//NoPosPlusRecord.o NoPosPlusRecord.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/general * compiling ParseTools.cpp g++ -c -o ../../../obj//ParseTools.o ParseTools.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 PushBackStreamBuf.cpp g++ -c -o ../../../obj//PushBackStreamBuf.o PushBackStreamBuf.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 CompressionTools.cpp g++ -c -o ../../../obj//CompressionTools.o CompressionTools.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 CommonHelp.cpp g++ -c -o ../../../obj//CommonHelp.o CommonHelp.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/gzstream g++ -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 RecordKeyVector.cpp g++ -c -o ../../../../obj//RecordKeyVector.o RecordKeyVector.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../../utils//lineFileUtilities/ -I../../../utils//FileRecordTools/FileReaders/ -I../../../utils//general/ -I../../../utils//fileType/ -I../../../utils//Contexts/ -I../../../utils//GenomeFile/ -I../../../utils//BamTools/include -I../../../utils//BamTools/src/ -I../../../utils//version/ - Building in src/utils/fileType * compiling fileType.cpp g++ -c -o ../../../obj//fileType.o fileType.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 FileRecordTypeChecker.cpp g++ -c -o ../../../obj//FileRecordTypeChecker.o FileRecordTypeChecker.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//BamTools/include/ -I../../utils//general - Building in src/utils/bedFilePE * compiling bedFilePE.cpp g++ -c -o ../../../obj//bedFilePE.o bedFilePE.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//lineFileUtilities/ -I../../utils//bedFile/ -I../../utils//gzstream/ -I../../utils//fileType/ * compiling ContextFisher.cpp g++ -c -o ../../../obj//ContextFisher.o ContextFisher.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 ContextMap.cpp g++ -c -o ../../../obj//ContextMap.o ContextMap.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 ContextSample.cpp g++ -c -o ../../../obj//ContextSample.o ContextSample.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 ContextSpacing.cpp g++ -c -o ../../../obj//ContextSpacing.o ContextSpacing.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 ContextMerge.cpp g++ -c -o ../../../obj//ContextMerge.o ContextMerge.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 ContextJaccard.cpp g++ -c -o ../../../obj//ContextJaccard.o ContextJaccard.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 ContextClosest.cpp g++ -c -o ../../../obj//ContextClosest.o ContextClosest.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/NewChromsweep * compiling NewChromsweep.cpp g++ -c -o ../../../obj//NewChromsweep.o NewChromsweep.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 ContextCoverage.cpp g++ -c -o ../../../obj//ContextCoverage.o ContextCoverage.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../../utils//general/ -I../../utils//lineFileUtilities/ -I../../utils//fileType/ -I../../utils//FileRecordTools/ -I../../utils//FileRecordTools/FileReaders/ -I../../utils//FileRecordTools/Records/ -I../../utils//KeyListOps/ -I../../utils//GenomeFile/ -I../../utils//BamTools/include -I../../utils//BamTools/src/ -I../../utils//version/ * compiling ContextComplement.cpp g++ -c -o ../../../obj//ContextComplement.o ContextComplement.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 ContextGroupBy.cpp g++ -c -o ../../../obj//ContextGroupBy.o ContextGroupBy.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 CloseSweep.cpp g++ -c -o ../../../obj//CloseSweep.o CloseSweep.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 KeyListOpsMethods.cpp g++ -c -o ../../../obj//KeyListOpsMethods.o KeyListOpsMethods.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/sequenceUtilities * compiling sequenceUtils.cpp g++ -c -o ../../../obj//sequenceUtils.o sequenceUtils.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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/tabFile * compiling tabFile.cpp g++ -c -o ../../../obj//tabFile.o tabFile.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I..//BamTools/include -I..//bedFile/ -I..//lineFileUtilities/ -I..//gzstream/ -I..//fileType/ -Lsrc/utils/BamTools//lib - Building in src/utils/BlockedIntervals * compiling BlockedIntervals.cpp g++ -c -o ../../../obj//BlockedIntervals.o BlockedIntervals.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I..//BamTools/include -I..//bedFile/ -I..//gzstream/ -I..//fileType/ -I..//lineFileUtilities/ -Lsrc/utils/BamTools//lib * compiling BamMultiReader.cpp g++ -c src/api/BamMultiReader.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 - Building in src/utils/Fasta * compiling Fasta.cpp g++ -c -o ../../../obj//Fasta.o Fasta.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 BamReader.cpp g++ -c src/api/BamReader.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 Fasta.cpp: In member function ‘std::__cxx11::string FastaReference::getSequence(std::__cxx11::string)’: Fasta.cpp:290:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(seq, sizeof(char), seqlen, file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fasta.cpp: In member function ‘std::__cxx11::string FastaReference::getSubSequence(std::__cxx11::string, int, int)’: Fasta.cpp:332:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(seq, sizeof(char), (off_t) seqlen, file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling BamWriter.cpp g++ -c src/api/BamWriter.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I..//BamTools/include -I..//bedFile/ -I..//lineFileUtilities/ -I..//gzstream/ -I..//fileType/ -Lsrc/utils/BamTools//lib * compiling SamHeader.cpp g++ -c src/api/SamHeader.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 - Building in src/utils/VectorOps * compiling VectorOps.cpp g++ -c -o ../../../obj//VectorOps.o VectorOps.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 SamProgram.cpp g++ -c src/api/SamProgram.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 split.cpp g++ -c -o ../../../obj//split.o split.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 SamProgramChain.cpp g++ -c src/api/SamProgramChain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamProgramChain.o * compiling SamReadGroup.cpp g++ -c src/api/SamReadGroup.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/SamReadGroup.o - Building in src/utils/GenomeFile * compiling GenomeFile.cpp g++ -c -o ../../../obj//GenomeFile.o GenomeFile.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/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/ 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 SamReadGroupDictionary.cpp g++ -c src/api/SamReadGroupDictionary.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 - Building in src/utils/RecordOutputMgr * compiling RecordOutputMgr.cpp g++ -c -o ../../../obj//RecordOutputMgr.o RecordOutputMgr.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 NewGenomeFile.cpp g++ -c -o ../../../obj//NewGenomeFile.o NewGenomeFile.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/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 SamSequence.cpp g++ -c src/api/SamSequence.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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/ToolBase * compiling ToolBase.cpp g++ -c -o ../../../obj//ToolBase.o ToolBase.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/ - Building in src/utils/driver * compiling BedtoolsDriver.cpp g++ -c -o ../../../obj//BedtoolsDriver.o BedtoolsDriver.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/ * compiling SamSequenceDictionary.cpp g++ -c src/api/SamSequenceDictionary.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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/annotateBed * compiling annotateMain.cpp g++ -c -o ../../obj//annotateMain.o annotateMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 BamHeader_p.cpp g++ -c src/api/internal/bam/BamHeader_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 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; ^~~~~~~~~~ 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; ^~~~~~~~~~~~~~~~~ - Building in src/bamToFastq * compiling bamToFastqMain.cpp g++ -c -o ../../obj//bamToFastqMain.o bamToFastqMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 BamMultiReader_p.cpp g++ -c src/api/internal/bam/BamMultiReader_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 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 annotateBed.cpp g++ -c -o ../../obj//annotateBed.o annotateBed.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 bamToFastq.cpp g++ -c -o ../../obj//bamToFastq.o bamToFastq.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/ - Building in src/bedToBam * compiling bedToBam.cpp g++ -c -o ../../obj//bedToBam.o bedToBam.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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; ^~~~~~~~~~~ - Building in src/bedToIgv * compiling bedToIgv.cpp g++ -c -o ../../obj//bedToIgv.o bedToIgv.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//version/ bedpeToBam.cpp: In function ‘int bedpetobam_main(int, char**)’: bedpeToBam.cpp:61:10: warning: variable ‘haveMapQual’ set but not used [-Wunused-but-set-variable] bool haveMapQual = false; ^~~~~~~~~~~ * compiling BamRandomAccessController_p.cpp g++ -c src/api/internal/bam/BamRandomAccessController_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/bam/BamRandomAccessController_p.o - Building in src/bed12ToBed6 * compiling bed12ToBed6.cpp g++ -c -o ../../obj//bed12ToBed6.o bed12ToBed6.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 clusterBed.cpp g++ -c -o ../../obj//clusterBed.o clusterBed.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/ 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 closestFile.cpp g++ -c -o ../../obj//closestFile.o closestFile.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/complementFile * compiling complementHelp.cpp g++ -c -o ../../obj//complementHelp.o complementHelp.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 complementFile.cpp g++ -c -o ../../obj//complementFile.o complementFile.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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/coverageFile * compiling coverageHelp.cpp g++ -c -o ../../obj//coverageHelp.o coverageHelp.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 coverageFile.cpp g++ -c -o ../../obj//coverageFile.o coverageFile.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/fastaFromBed * compiling fastaFromBedMain.cpp g++ -c -o ../../obj//fastaFromBedMain.o fastaFromBedMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 BamIndexFactory_p.cpp g++ -c src/api/internal/index/BamIndexFactory_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 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 BamStandardIndex_p.cpp g++ -c src/api/internal/index/BamStandardIndex_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 * compiling fastaFromBed.cpp g++ -c -o ../../obj//fastaFromBed.o fastaFromBed.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 genomeCoverageBed.cpp g++ -c -o ../../obj//genomeCoverageBed.o genomeCoverageBed.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 flankBed.cpp g++ -c -o ../../obj//flankBed.o flankBed.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/ 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 BamToolsIndex_p.cpp g++ -c src/api/internal/index/BamToolsIndex_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/index/BamToolsIndex_p.o * compiling BamDeviceFactory_p.cpp g++ -c src/api/internal/io/BamDeviceFactory_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 BamFile_p.cpp g++ -c src/api/internal/io/BamFile_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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/getOverlap * compiling getOverlap.cpp g++ -c -o ../../obj//getOverlap.o getOverlap.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 BamFtp_p.cpp g++ -c src/api/internal/io/BamFtp_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 - Building in src/groupBy * compiling groupBy.cpp g++ -c -o ../../obj//groupBy.o groupBy.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/ 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 BamHttp_p.cpp g++ -c src/api/internal/io/BamHttp_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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/intersectFile * compiling intersectHelp.cpp g++ -c -o ../../obj//intersectHelp.o intersectHelp.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 groupByHelp.cpp g++ -c -o ../../obj//groupByHelp.o groupByHelp.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 intersectFile.cpp g++ -c -o ../../obj//intersectFile.o intersectFile.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 BamPipe_p.cpp g++ -c src/api/internal/io/BamPipe_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 BgzfStream_p.cpp g++ -c src/api/internal/io/BgzfStream_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 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 ByteArray_p.cpp g++ -c src/api/internal/io/ByteArray_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/ByteArray_p.o - Building in src/fisher * compiling fisherHelp.cpp g++ -c -o ../../obj//fisherHelp.o fisherHelp.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/jaccard * compiling jaccardHelp.cpp g++ -c -o ../../obj//jaccardHelp.o jaccardHelp.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 fisher.cpp g++ -c -o ../../obj//fisher.o fisher.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 jaccard.cpp g++ -c -o ../../obj//jaccard.o jaccard.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 HostAddress_p.cpp g++ -c src/api/internal/io/HostAddress_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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) | ^~ * compiling HostInfo_p.cpp g++ -c src/api/internal/io/HostInfo_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 - Building in src/linksBed * compiling linksMain.cpp g++ -c -o ../../obj//linksMain.o linksMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 HttpHeader_p.cpp g++ -c src/api/internal/io/HttpHeader_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 kfunc.cpp g++ -c -o ../../obj//kfunc.o kfunc.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 ILocalIODevice_p.cpp g++ -c src/api/internal/io/ILocalIODevice_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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/maskFastaFromBed * compiling maskFastaFromBedMain.cpp g++ -c -o ../../obj//maskFastaFromBedMain.o maskFastaFromBedMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 RollingBuffer_p.cpp g++ -c src/api/internal/io/RollingBuffer_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 linksBed.cpp g++ -c -o ../../obj//linksBed.o linksBed.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 TcpSocketEngine_p.cpp g++ -c src/api/internal/io/TcpSocketEngine_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/TcpSocketEngine_p.o * compiling TcpSocketEngine_unix_p.cpp g++ -c src/api/internal/io/TcpSocketEngine_unix_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/io/TcpSocketEngine_unix_p.o * compiling TcpSocket_p.cpp g++ -c src/api/internal/io/TcpSocket_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 SamFormatParser_p.cpp g++ -c src/api/internal/sam/SamFormatParser_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/sam/SamFormatParser_p.o - Building in src/mapFile * compiling mapHelp.cpp g++ -c -o ../../obj//mapHelp.o mapHelp.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 SamFormatPrinter_p.cpp g++ -c src/api/internal/sam/SamFormatPrinter_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 mapFile.cpp g++ -c -o ../../obj//mapFile.o mapFile.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/mergeFile * compiling mergeHelp.cpp g++ -c -o ../../obj//mergeHelp.o mergeHelp.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 SamHeaderValidator_p.cpp g++ -c src/api/internal/sam/SamHeaderValidator_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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 - Building in src/multiBamCov * compiling multiBamCovMain.cpp g++ -c -o ../../obj//multiBamCovMain.o multiBamCovMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 mergeFile.cpp g++ -c -o ../../obj//mergeFile.o mergeFile.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/ multiBamCovMain.cpp: In function ‘int multibamcov_main(int, char**)’: multiBamCovMain.cpp:38:10: warning: variable ‘haveBed’ set but not used [-Wunused-but-set-variable] bool haveBed = false; ^~~~~~~ multiBamCovMain.cpp:39:10: warning: variable ‘haveBams’ set but not used [-Wunused-but-set-variable] bool haveBams = false; ^~~~~~~~ multiBamCovMain.cpp:47:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ * compiling BamException_p.cpp g++ -c src/api/internal/utils/BamException_p.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -Isrc/ -Iinclude/ -o src/api/internal/utils/BamException_p.o - Building in src/multiIntersectBed * compiling multiIntersectBedMain.cpp g++ -c -o ../../obj//multiIntersectBedMain.o multiIntersectBedMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 multiIntersectBed.cpp g++ -c -o ../../obj//multiIntersectBed.o multiIntersectBed.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 multiBamCov.cpp g++ -c -o ../../obj//multiBamCov.o multiBamCov.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/ * 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 - Building in src/nucBed * compiling nucBedMain.cpp g++ -c -o ../../obj//nucBedMain.o nucBedMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/ multiIntersectBedMain.cpp: In function ‘int multiintersect_main(int, char**)’: multiIntersectBedMain.cpp:45:10: warning: variable ‘haveFiles’ set but not used [-Wunused-but-set-variable] bool haveFiles = false; ^~~~~~~~~ multiIntersectBedMain.cpp:47:10: warning: variable ‘haveGenome’ set but not used [-Wunused-but-set-variable] bool haveGenome = false; ^~~~~~~~~~ multiIntersectBedMain.cpp:48:10: warning: variable ‘haveFiller’ set but not used [-Wunused-but-set-variable] bool haveFiller = true; ^~~~~~~~~~ * compiling nucBed.cpp g++ -c -o ../../obj//nucBed.o nucBed.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//sequenceUtilities/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//Fasta/ -I../utils//version/ - Building in src/pairToBed * compiling pairToBedMain.cpp g++ -c -o ../../obj//pairToBedMain.o pairToBedMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 pairToBed.cpp g++ -c -o ../../obj//pairToBed.o pairToBed.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/ 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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFilePE/ -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//version/ -I../utils//fileType/ -I../utils//version/ - Building in src/randomBed * compiling randomBedMain.cpp g++ -c -o ../../obj//randomBedMain.o randomBedMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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; ^~~~~~~~~~ pairToPairMain.cpp: In function ‘int pairtopair_main(int, char**)’: pairToPairMain.cpp:44:10: warning: variable ‘haveFraction’ set but not used [-Wunused-but-set-variable] bool haveFraction = false; ^~~~~~~~~~~~ * compiling randomBed.cpp g++ -c -o ../../obj//randomBed.o randomBed.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//version/ - Building in src/regressTest compiling RegressTest.cpp g++ -c -o ../../obj//RegressTest.o RegressTest.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general * compiling pairToPair.cpp g++ -c -o ../../obj//pairToPair.o pairToPair.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFilePE/ -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//version/ -I../utils//fileType/ -I../utils//version/ - Building in src/reldist * compiling reldistMain.cpp g++ -c -o ../../obj//reldistMain.o reldistMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/ RegressTest.cpp: In member function ‘bool RegressTest::executeAndCompareCorrectness(const fileListType&)’: RegressTest.cpp:431:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(diffCmd.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function ‘bool RegressTest::startMemoryProfile(bool)’: RegressTest.cpp:573:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function ‘bool RegressTest::calcMemoryStats()’: RegressTest.cpp:622:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ pairToPair.cpp: In member function ‘void PairToPair::FindOverlaps(const BEDPE&)’: pairToPair.cpp:112:14: warning: variable ‘found1’ set but not used [-Wunused-but-set-variable] bool found1 = false; ^~~~~~ pairToPair.cpp:113:14: warning: variable ‘found2’ set but not used [-Wunused-but-set-variable] bool found2 = false; ^~~~~~ * compiling reldist.cpp g++ -c -o ../../obj//reldist.o reldist.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/ 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", ^~~~~~~~~~~~~~~~~~~~~~~~ reldist.cpp:71:16: 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/sampleFile * compiling sampleHelp.cpp g++ -c -o ../../obj//sampleHelp.o sampleHelp.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 regressTestMain.cpp g++ -c -o ../../obj//regressTestMain.o regressTestMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 sampleFile.cpp g++ -c -o ../../obj//sampleFile.o sampleFile.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/shuffleBed * compiling shuffleBedMain.cpp g++ -c -o ../../obj//shuffleBedMain.o shuffleBedMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 shiftBed.cpp g++ -c -o ../../obj//shiftBed.o shiftBed.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/sortBed * compiling sortMain.cpp g++ -c -o ../../obj//sortMain.o sortMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/spacingFile * compiling spacingHelp.cpp g++ -c -o ../../obj//spacingHelp.o spacingHelp.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/ 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) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ slopBed.cpp:91:47: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘CHRPOS’ {aka ‘unsigned int’} [-Wsign-compare] if ( ((int)bed.end + (long)_leftSlop) <= chromSize ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ slopBed.cpp:108:52: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘CHRPOS’ {aka ‘unsigned int’} [-Wsign-compare] if( ((int)bed.start - (long)_leftSlop) >= chromSize && _leftSlop < 0) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/split * compiling splitBed.cpp g++ -c -o ../../obj//splitBed.o splitBed.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 splitBedMain.cpp g++ -c -o ../../obj//splitBedMain.o splitBedMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//version/ - Building in src/subtractFile * compiling subtractHelp.cpp g++ -c -o ../../obj//subtractHelp.o subtractHelp.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//Contexts/ -I../utils//general/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//GenomeFile/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//BlockedIntervals -I../utils//BamTools-Ancillary -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders/ -I../utils//FileRecordTools/Records/ -I../utils//KeyListOps/ -I../utils//RecordOutputMgr/ -I../utils//NewChromsweep -I../utils//BinTree -I../utils//version/ -I../utils//ToolBase/ -I../../src//intersectFile/ * compiling subtractFile.cpp g++ -c -o ../../obj//subtractFile.o subtractFile.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/ - Building in src/unionBedGraphs * compiling unionBedGraphsMain.cpp g++ -c -o ../../obj//unionBedGraphsMain.o unionBedGraphsMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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; ^~~~~~~~~~ * compiling tagBam.cpp g++ -c -o ../../obj//tagBam.o tagBam.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/windowBed * compiling windowMain.cpp g++ -c -o ../../obj//windowMain.o windowMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//genomeFile/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I../utils//BamTools/include -I../utils//BamTools-Ancillary -I../utils//version/ - Building in src/windowMaker * compiling windowMakerMain.cpp g++ -c -o ../../obj//windowMakerMain.o windowMakerMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//GenomeFile/ -I../utils//bedFile/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//lineFileUtilities/ -I../utils//BamTools/include -I../utils//version/ * compiling windowBed.cpp g++ -c -o ../../obj//windowBed.o windowBed.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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 windowMaker.cpp g++ -c -o ../../obj//windowMaker.o windowMaker.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/ - Building main bedtools binary. done. - Creating executables for old CLI. done. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' mv test/shuffle debian/ dh_auto_test make -j4 test make[2]: Entering directory '/<>/bedtools-2.27.1+dfsg' $CXXFLAGS is [-g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11] Building BEDTools: ========================================================= * Creating BamTools API DETECTED_VERSION = v2.27.1 CURRENT_VERSION = v2.27.1 - Building in src/utils/FileRecordTools/FileReaders - Building in src/utils/FileRecordTools/Records - Building in src/utils/FileRecordTools - Building in src/utils/bedFile make[3]: Nothing to be done for 'all'. make[3]: '../../../obj//bedFile.o' is up to date. make[3]: Nothing to be done for 'all'. - Building in FileReaders - Building in src/utils/version - Building in src/utils/BinTree - Building in src/utils/bedGraphFile make[4]: Nothing to be done for 'all'. - Building in Records make[3]: '../../../obj//BinTree.o' is up to date. make[4]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. make[3]: '../../../obj//bedGraphFile.o' is up to date. - Building in src/utils/chromsweep - Building in src/utils/Contexts - Building in src/utils/general - Building in src/utils/gzstream make[3]: '../../../obj//chromsweep.o' is up to date. make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. make[3]: '../../../obj//gzstream.o' is up to date. - Building in src/utils/fileType - Building in src/utils/bedFilePE - Building in src/utils/KeyListOps - Building in src/utils/NewChromsweep make[3]: Nothing to be done for 'all'. make[3]: '../../../obj//bedFilePE.o' is up to date. - Building in src/utils/sequenceUtilities make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/utils/tabFile - Building in src/utils/BamTools make[3]: '../../../obj//sequenceUtils.o' is up to date. make[3]: '../../../obj//tabFile.o' is up to date. - Building in src/utils/BamTools-Ancillary - Building in src/utils/BlockedIntervals - Building in src/utils/Fasta 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/utils/VectorOps make[3]: Nothing to be done for 'all'. - Building in src/utils/GenomeFile - Building in src/utils/RecordOutputMgr - Building in src/utils/ToolBase make[3]: '../../../obj//VectorOps.o' is up to date. make[3]: '../../../obj//ToolBase.o' is up to date. make[3]: '../../../obj//RecordOutputMgr.o' is up to date. - Building in src/utils/driver make[3]: '../../../obj//NewGenomeFile.o' is up to date. - Building in src/annotateBed - Building in src/bamToBed - Building in src/bamToFastq 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/bedToBam - Building in src/bedToIgv - Building in src/bedpeToBam 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'. make[3]: Nothing to be done for 'all'. - Building in src/clusterBed - Building in src/closestFile - Building in src/complementFile 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/coverageFile - Building in src/expand make[3]: Nothing to be done for 'all'. - Building in src/fastaFromBed make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/genomeCoverageBed - Building in src/flankBed - Building in src/getOverlap make[3]: Nothing to be done for 'all'. - 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/fisher - Building in src/intersectFile make[3]: Nothing to be done for 'all'. - Building in src/jaccard - Building in src/linksBed 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/mapFile - Building in src/maskFastaFromBed 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'. make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. - Building in src/nucBed - Building in src/multiIntersectBed - Building in src/pairToBed - Building in src/pairToPair make[3]: Nothing to be done for 'all'. 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/regressTest - Building in src/randomBed - Building in src/reldist - Building in src/sampleFile make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. compiling RegressTest.cpp g++ -c -o ../../obj//RegressTest.o RegressTest.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general make[3]: Nothing to be done for 'all'. - Building in src/shuffleBed - Building in src/shiftBed - Building in src/slopBed 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/spacingFile - Building in src/sortBed - Building in src/split 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/subtractFile - Building in src/tagBam - Building in src/unionBedGraphs 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/windowBed - Building in src/windowMaker make[3]: Nothing to be done for 'all'. make[3]: Nothing to be done for 'all'. RegressTest.cpp: In member function ‘bool RegressTest::executeAndCompareCorrectness(const fileListType&)’: RegressTest.cpp:431:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(diffCmd.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function ‘bool RegressTest::startMemoryProfile(bool)’: RegressTest.cpp:573:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function ‘bool RegressTest::calcMemoryStats()’: RegressTest.cpp:622:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ compiling regressTestMain.cpp g++ -c -o ../../obj//regressTestMain.o regressTestMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general - Building main bedtools binary. done. - Creating executables for old CLI. done. Testing bedtools bamtobed: bamtobed.t1...ok bamtobed.t2...ok bamtobed.t3...ok bamtobed.t4...ok bamtobed.t5...ok bamtobed.t6...ok bamtobed.t7...ok bamtobed.t8...ok bamtobed.t9...ok bamtobed.t10...ok bamtobed.t9...ok bamtobed.t11...ok Testing bedtools bamtofastq: ok ok Testing bedtools bed12tobed6: bed12tobed6.t1...ok bed12tobed6.t2...ok bed12tobed6.t3...ok bed12tobed6.t4...ok bed12tobed6.t5...ok Testing bedtools closest: closest.t1...ok closest.t2...ok closest.t3...ok closest.t4...ok closest.t5...ok closest.t6...ok closest.t7...ok closest.t8...ok closest.t9...ok closest.t10...ok closest.t11...ok closest.t13...ok closest.t14...ok closest.t15...ok closest.t16...ok closest.t17...ok closest.t18...ok closest.t19...ok closest.t20...ok closest.t21...ok closest.t22...ok closest.t23...ok closest.t24...ok closest.t25...ok closest.t26...ok closest.t27...ok closest.t28...ok closest.t29...ok closest.t30...ok closest.t31...ok closest.t32...ok closest.t33...ok closest.t34...ok closest.t35...ok closest.t36...ok closest.t37...ok closest.t38...ok closest.t39...ok closest.t40...ok closest.t41...ok closest.t42...ok closest.t43...ok closest.t44...ok closest.t45...ok closest.t46...ok closest.t47...ok closest.t48...ok closest.t49...ok closest.t50...ok closest.t51...ok closest.t52...ok closest.t53...ok closest.t54...ok closest.t55...ok closest.t56...ok closest.t57...ok closest.t58...ok closest.t59...ok closest.t60...ok closest.t61...ok closest.t62...ok closest.t63...ok closest.t64...ok closest.t65...ok closest.t66...ok closest.t67...ok closest.t68...ok closest.t69...ok closest.t70...ok closest.t71...ok ########################################################### # # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS # ########################################################### closest.t01...ok closest.t02...ok closest.t03...ok closest.t04...ok closest.t05...ok closest.t06...ok closest.t07...ok closest.t08...ok closest.t09...ok closest.t10...ok closest.t11...ok closest.t12...ok closest.t13...ok closest.t14...ok closest.t15...ok closest.t16...ok closest.t17...ok closest.t18...ok closest.t19...ok closest.20...ok closest.21...ok closest.22...ok closest.23...ok ########################################################### # # K CLOSEST HITS TESTS # ########################################################### kclosest.t1...ok kclosest.t2...ok kclosest.t3...ok kclosest.t4...ok kclosest.t5...ok kclosest.t6...ok kclosest.t7...ok kclosest.t8...ok kclosest.t9...ok kclosest.t10...ok kclosest.t11...ok kclosest.t12...ok kclosest.t13...ok kclosest.t14...ok kclosest.t15...ok kclosest.t16...ok kclosest.t17...ok kclosest.t18...ok kclosest.t19...ok kclosest.t20...ok kclosest.t21...ok kclosest.t22...ok kclosest.t23...ok kclosest.t24...ok kclosest.t25...ok kclosest.t26...ok kclosest.t27...ok kclosest.t28...ok kclosest.t29...ok kclosest.t30...ok kclosest.t31...ok kclosest.t32...ok kclosest.t33...ok kclosest.t34...ok kclosest.t35...ok kclosest.t36...ok kclosest.t37...ok kclosest.t38...ok kclosest.t39...ok kclosest.t40...ok kclosest.t41...ok kclosest.t42...ok kclosest.t43...ok kclosest.t44...ok kclosest.t45...ok Testing bedtools cluster: cluster.t1...ok cluster.t2...ok Testing bedtools complement: complement.t1...ok complement.t2...ok complement.t3...ok complement.t4...ok complement.t5...ok complement.t6...ok complement.t7...ok complement.t8...ok complement.t9...ok Testing bedtools coverage: coverage.t1...ok coverage.t1b...ok coverage.t2...ok coverage.t2b...ok coverage.t3...ok coverage.t3b...ok coverage.t4...ok coverage.t4b...ok coverage.t5...ok coverage.t5b...ok coverage.t6...ok coverage.t6b...ok coverage.t7...ok coverage.t7b...ok coverage.t8...ok coverage.t8b...ok coverage.t9...ok coverage.t9b...ok coverage.t10...ok coverage.t10b...ok coverage.t11...ok coverage.t11b...ok coverage.t12...ok coverage.t12b...ok coverage.t13...ok coverage.t13b...ok coverage.t14...ok coverage.t14b...ok coverage.t15...ok coverage.t15b...ok coverage.t16...ok coverage.t16b...ok coverage.t17...ok coverage.t17b...ok coverage.t18...ok coverage.t18b...ok coverage.t19...ok coverage.t19b...ok coverage.t20...ok Testing bedtools expand: expand.t1...ok expand.t2...ok expand.t3...ok Testing bedtools fisher: fisher.t1...ok fisher.t2...ok fisher.t3...ok fisher.t4...ok Testing bedtools flank: flank.t1...ok flank.t2...ok flank.t3...ok flank.t4...ok flank.t5...ok flank.t6...ok flank.t7...ok flank.t8...ok flank.t9...ok flank.t10...ok flank.t11...ok Testing bedtools general: general.t01...ok general.t02...ok general.t03...ok general.t05...ok general.t06...ok general.t07...ok general.t08...ok general.t09...ok general.t10...ok general.t11...ok general.t12...ok general.t13...ok general.t14...ok general.15...ok general.t16...ok general.t17...ok general.t18...ok general.t19...ok general.t20...ok general.t21...ok general.22...ok general.t23...ok general.t24...ok general.t25...ok general.t26...ok general.t27...ok general.t28...ok general.29...ok general.t30...ok general.t31...ok general.t32...ok general.t33...ok general.t34...ok general.t35...ok general.36...ok general.t37...ok general.t38...ok general.t39...ok general.t40...ok general.t41...ok general.t42...ok general.t43...ok general.t44...ok general.t45...ok general.t46...ok Testing bedtools genomecov: genomecov.t1...ok genomecov.t2...ok genomecov.t3...ok genomecov.t4...ok genomecov.t5...ok genomecov.t6...ok genomecov.t7...ok genomecov.t8...ok genomecov.t9...ok genomecov.t10...ok genomecov.t11...ok genomecov.t12...ok genomecov.t13...ok genomecov.t14...ok genomecov.t15...ok Testing bedtools getfasta: getfasta.t01...ok getfasta.t02...ok getfasta.t03...ok getfasta.t04...ok getfasta.t05...ok getfasta.t06...ok getfasta.t07...ok getfasta.t08...index file test.iupac.fa.fai not found, generating... ok getfasta.t09...index file test.iupac.fa.fai not found, generating... ok getfasta.t10...index file test.fa.fai not found, generating... ok getfasta.t11...ok getfasta.t12...ok getfasta.t13...ok getfasta.t14...ok getfasta.t15...ok getfasta.t134..ok Testing bedtools groupby: groupby.t1...ok groupby.t2...ok groupby.t3...ok groupby.t4...ok groupby.t5...ok groupby.t6...ok groupby.t7...ok groupby.t8...ok groupby.t9...ok groupby.t10...ok groupby.t11...ok groupby.t12...ok groupby.t13...ok groupby.t14...ok groupby.t16...ok groupby.t17...ok groupby.t18...ok groupby.t19...\c ok groupby.t20...\c ok Testing bedtools intersect: intersect.t01...ok intersect.t02...ok intersect.t03...ok intersect.t04...ok intersect.t05...ok intersect.t06...ok intersect.t07...ok intersect.t08...ok intersect.t09...ok intersect.t10...ok intersect.t11...ok intersect.t12...ok intersect.t13...ok intersect.t14...ok intersect.t15...ok intersect.t16...ok intersect.t17...ok intersect.t18...ok intersect.t19...ok intersect.t20...ok intersect.t21...ok intersect.t22...ok intersect.t22.a...ok intersect.t22.b...ok intersect.t22.c...ok intersect.t22.d...ok intersect.t22.e...ok intersect.t22.f...ok intersect.t22.g...ok intersect.t23...ok intersect.t24...ok intersect.t25...ok intersect.t26...ok intersect.t27...ok intersect.t28...ok intersect.t29...ok intersect.t30...ok intersect.t31...ok intersect.t32...ok intersect.t33...ok intersect.t34...ok intersect.t35...ok intersect.t36...ok intersect.t37...ok intersect.t38...ok intersect.t39...ok intersect.t40...ok intersect.t41...ok intersect.t42...ok intersect.t43...ok intersect.t44...ok intersect.t45...ok intersect.t46...ok intersect.t47...ok intersect.t48...ok intersect.t49...ok intersect.t50...ok intersect.t51...ok intersect.t52...ok intersect.t53...ok intersect.t54...ok intersect.t55...ok intersect.t56...ok intersect.t57...ok intersect.t58...ok intersect.t59...ok intersect.t60...ok intersect.t61...ok intersect.t62...ok intersect.t63...ok intersect.t64...ok intersect.t65...ok intersect.t66...ok intersect.t67...ok intersect.t68...ok intersect.t69...ok intersect.t70...ok intersect.t71...ok intersect.t72...ok intersect.t73...ok intersect.t74...ok intersect.t75...ok intersect.t76...ok intersect.t77...ok intersect.t78...ok intersect.t79...ok intersect.t80...ok intersect.t81...ok intersect.t82...ok intersect.new.t01...ok intersect.new.t02...ok intersect.new.t03...ok intersect.new.t04...ok intersect.new.t05...ok intersect.new.t06...ok intersect.new.t07...ok intersect.new.t08...ok intersect.new.t09...ok intersect.new.t10...ok intersect.new.t11...ok intersect.new.t12...ok intersect.new.t13...ok intersect.new.t14...ok intersect.new.t15...ok intersect.new.t16...ok intersect.new.t17...ok intersect.new.t18...ok intersect.new.t19...ok intersect.new.t20...ok intersect.new.t20.b...ok intersect.new.t20.c...ok intersect.new.t21...ok intersect.new.t22...ok intersect.new.t23...ok intersect.new.t24...ok intersect.new.t25...ok intersect.new.t26...ok intersect.new.t27...ok intersect.new.t28...ok intersect.new.t29...ok intersect.new.t30...ok intersect.new.t31...ok intersect.new.t32...ok intersect.new.t33...ok intersect.new.t34...ok intersect.new.t35...ok intersect.new.t36...ok intersect.new.t37...ok intersect.new.t38...ok intersect.new.t39...ok intersect.new.t40...ok intersect.new.t41...ok intersect.new.t42...ok intersect.new.t43...ok intersect.new.t44...ok intersect.new.t45...ok intersect.new.t46...ok intersect.new.t47...ok intersect.new.t48...ok intersect.new.t49...ok intersect.new.t50...ok intersect.new.t51...ok intersect.new.t52...ok intersect.new.t53...ok intersect.new.t54...ok intersect.new.t55...ok intersect.new.t56...ok intersect.new.t57...ok intersect.new.t58...ok intersect.new.t59...ok intersect.new.t60...ok intersect.new.t61...ok intersect.new.t62...ok intersect.new.t63...ok intersect.new.t64...ok intersect.new.t65...ok intersect.new.t66...ok intersect.new.t67a...ok intersect.new.t67b...ok intersect.new.t68a...ok intersect.new.t68b...ok intersect.new.t69...ok intersect.new.t70...ok intersect.new.t71...ok intersect.new.t72...ok ########################################################### # # MULTIPLE DATABASE INTERSECTION # ########################################################### intersect.t01...ok intersect.t02...ok intersect.t03...ok intersect.t04...ok intersect.t05...ok intersect.t06...ok intersect.t07...ok intersect.t08...ok intersect.t09...ok intersect.t10...ok intersect.t11...ok intersect.t12...ok intersect.t13...ok intersect.t13...ok intersect.t14...ok intersect.t15...ok intersect.t16...ok intersect.t17...ok intersect.t18...ok intersect.t19...ok ########################################################### # # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS # ########################################################### intersect.t01...ok intersect.t02...ok intersect.t03...ok intersect.t04...ok intersect.t05...ok intersect.t06...ok intersect.t07...ok intersect.t08...ok intersect.t09...ok intersect.t10...ok intersect.t11...ok intersect.t12...ok intersect.t13...ok intersect.t14...ok intersect.t15...ok intersect.t16...ok intersect.t17...ok intersect.t18...ok intersect.t19...ok intersect.20...ok intersect.21...ok intersect.22...ok intersect.23...ok Testing bedtools jaccard: jaccard.t01...ok jaccard.t02...ok jaccard.t03...ok jaccard.t05...ok jaccard.t06...ok jaccard.t07...ok jaccard.t08...ok jaccard.t09...ok jaccard.t10...ok jaccard.t11...ok jaccard.t12...ok jaccard.t13...ok Testing bedtools makewindows: makewindows.t01...ok makewindows.t02...ok makewindows.t03...ok makewindows.t04...ok makewindows.t05...ok makewindows.t06...ok makewindows.t07...ok makewindows.t08...ok makewindows.t09...ok Testing bedtools map: map.t01...ok map.t02...ok map.t03...ok map.t04...ok map.t05...ok map.t06...ok map.t07...ok map.t08...ok map.t09...ok map.t10...ok map.t11...ok map.t12...ok map.t13...ok map.t14...ok map.t15...ok map.t16...ok map.t17...ok map.t18...ok map.t19...ok map.t20...ok map.t21...ok map.t22..ok map.t23..ok map.t24..ok map.t25..ok map.t26..ok map.t27..ok map.t28..ok map.t29..ok map.t30..ok map.t31..ok map.t32..ok map.t33..ok map.t33..ok map.t33..ok map.t34..ok map.t35..ok map.t36..ok map.t37..ok map.t38..ok map.t39..ok map.t40..ok map.t41..ok map.t42..ok map.t43..ok map.t44...ok map.t45...ok map.t46...ok map.t47...ok map.t48...ok map.t49...ok map.t50...ok map.t51...ok map.t52...ok map.t53...ok map.t54...ok map.t55...ok Testing bedtools merge: merge.t1...ok merge.t2...ok merge.t3...ok merge.t4...ok merge.t5...ok merge.t6...ok merge.t7...ok merge.t8...ok merge.t9a...ok merge.t9b...ok merge.t10...ok merge.t11...ok merge.t12...ok merge.t13...ok merge.t14...ok merge.t15...ok merge.t16...ok merge.t17...ok merge.t18...ok merge.t19...ok merge.t20...ok merge.t21...ok merge.t22...ok merge.t23a...ok merge.t23b...ok merge.t24...ok merge.t25...ok merge.t26...ok merge.t27...ok merge.t28...ok merge.t29...ok merge.t30...ok merge.t31...ok merge.t32...ok merge.t33...ok merge.t34...ok merge.t35...ok merge.t36...ok merge.t37...ok merge.t38...ok merge.t39...ok merge.t40...ok merge.t41...ok merge.t42...ok merge.t43...ok merge.t44a...ok merge.t44b...skipped - could not find vcfSVtest.2.vcf merge.t45...ok merge.t46...ok merge.t47...ok merge.t48...ok merge.t49...ok Testing bedtools multicov: multicov.t1...ok multicov.t2...ok multicov.t3...ok multicov.t4...ok multicov.t5...ok multicov.t6...ok multicov.t7...ok multicov.t8...ok multicov.t9...ok Testing bedtools negativecontrol: Testing bedtools reldist: reldist.t01...ok reldist.t02...ok reldist.t03...ok Testing bedtools sample: sample.t01...ok sample.new.t02...ok sample.new.t03...ok sample.new.t04...ok sample.new.t05...ok sample.new.t06...ok sample.new.t07...ok sample.new.t08...ok sample.new.t09...ok Testing bedtools shift: shift.t1...ok shift.t2...ok shift.t3...ok shift.t3...ok shift.t4...ok shift.t5...ok shift.t6...ok shift.t7...ok shift.t8...ok shift.t9...ok shift.t10...ok Testing bedtools slop: slop.t1...ok slop.t2...ok slop.t3...ok slop.t4...ok slop.t5...ok slop.t6...ok slop.t7...ok slop.t8...ok slop.t9...ok slop.t10...ok slop.t11...ok slop.t12...ok slop.t13...ok slop.t14...ok slop.t15...ok slop.t16...ok slop.t17...ok slop.t18...ok slop.t19...ok slop.t20...ok slop.t21...ok slop.t22...ok Testing bedtools sort: sort.t01...ok sort.t02...ok sort.t03...ok sort.t04...ok sort.t05...ok sort.t06...ok sort.t07...ok sort.t08...ok sort.t09...ok sort.t10...ok Testing bedtools spacing: spacing.t01...ok Testing bedtools split: split.01.size...ok split.02.simple...ok spliit.03.simple...ok Testing bedtools subtract: subtract.t1...ok subtract.t2...ok subtract.t3...ok subtract.t4...ok subtract.t5...ok subtract.t6...ok subtract.t7...ok subtract.t8...ok subtract.t9...ok subtract.t10...ok subtract.t11...ok subtract.t12...ok subtract.t13...ok subtract.t14...ok subtract.t15...ok subtract.t16...ok subtract.t17...ok subtract.t18...ok subtract.t19...ok subtract.t20...ok subtract.t21...ok -------------------------- Test Results -------------------------- Tools passing: bamtobed bamtofastq bed12tobed6 closest cluster complement coverage expand fisher flank general genomecov getfasta groupby intersect jaccard makewindows map merge multicov reldist sample shift slop sort spacing split subtract Tools failing: negativecontrol NB: the 'negativecontrol' test is supposed to fail. If it wasn't caught, something went wrong with this test script. make[2]: Leaving directory '/<>/bedtools-2.27.1+dfsg' mv debian/shuffle test/ make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a rm -f -- debian/bedtools.substvars rm -fr -- debian/.debhelper/generated/bedtools/ debian/bedtools/ debian/tmp/ dh_auto_install -a install -d /<>/bedtools-2.27.1\+dfsg/debian/tmp make -j4 install DESTDIR=/<>/bedtools-2.27.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' $CXXFLAGS is [-g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11] Building BEDTools: ========================================================= * Creating BamTools API DETECTED_VERSION = v2.27.1 CURRENT_VERSION = v2.27.1 - Building in src/utils/FileRecordTools - Building in src/utils/FileRecordTools/Records - Building in src/utils/FileRecordTools/FileReaders - Building in src/utils/bedFile make[2]: '../../../obj//bedFile.o' is up to date. make[2]: Nothing to be done for 'all'. - Building in FileReaders - Building in src/utils/BinTree - Building in src/utils/version make[3]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in Records make[2]: '../../../obj//BinTree.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//bedGraphFile.o' is up to date. make[2]: '../../../obj//chromsweep.o' is up to date. - Building in src/utils/general - Building in src/utils/gzstream make[3]: Nothing to be done for 'all'. - Building in src/utils/fileType make[2]: Nothing to be done for 'all'. make[2]: '../../../obj//gzstream.o' is up to date. make[2]: Nothing to be done for 'all'. - Building in src/utils/KeyListOps - Building in src/utils/bedFilePE - Building in src/utils/NewChromsweep make[2]: Nothing to be done for 'all'. make[2]: '../../../obj//bedFilePE.o' is up to date. - Building in src/utils/sequenceUtilities make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in src/utils/tabFile - Building in src/utils/BamTools - Building in src/utils/BamTools-Ancillary make[2]: '../../../obj//tabFile.o' is up to date. make[2]: '../../../obj//sequenceUtils.o' is up to date. - Building in src/utils/BlockedIntervals - Building in src/utils/Fasta make[2]: Nothing to be done for 'all'. - Building in src/utils/VectorOps 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/utils/GenomeFile - Building in src/utils/RecordOutputMgr - Building in src/utils/ToolBase make[2]: '../../../obj//VectorOps.o' is up to date. make[2]: '../../../obj//NewGenomeFile.o' is up to date. make[2]: '../../../obj//RecordOutputMgr.o' is up to date. make[2]: '../../../obj//ToolBase.o' is up to date. - Building in src/utils/driver - Building in src/annotateBed - Building in src/bamToBed - Building in src/bamToFastq 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/bedToBam make[2]: Nothing to be done for 'all'. - Building in src/bedpeToBam - Building in src/bed12ToBed6 - Building in src/bedToIgv 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/closestFile make[2]: Nothing to be done for 'all'. - Building in src/clusterBed - Building in src/complementFile - Building in src/coverageFile make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in src/expand - Building in src/fastaFromBed - Building in src/genomeCoverageBed - Building in src/flankBed 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/getOverlap make[2]: Nothing to be done for 'all'. - Building in src/intersectFile - Building in src/groupBy - Building in src/fisher make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in src/jaccard make[2]: Nothing to be done for 'all'. - Building in src/linksBed - Building in src/maskFastaFromBed 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'. make[2]: Nothing to be done for 'all'. - Building in src/mergeFile - Building in src/multiBamCov make[2]: Nothing to be done for 'all'. - Building in src/multiIntersectBed - Building in src/nucBed make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in src/pairToBed - Building in src/pairToPair - Building in src/randomBed - Building in src/regressTest make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in src/reldist compiling RegressTest.cpp g++ -c -o ../../obj//RegressTest.o RegressTest.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/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/sampleFile - Building in src/shiftBed 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/shuffleBed - Building in src/slopBed - Building in src/sortBed 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/spacingFile - Building in src/subtractFile - Building in src/split make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. - Building in src/tagBam make[2]: Nothing to be done for 'all'. - Building in src/unionBedGraphs - Building in src/windowBed make[2]: Nothing to be done for 'all'. - Building in src/windowMaker make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. RegressTest.cpp: In member function ‘bool RegressTest::executeAndCompareCorrectness(const fileListType&)’: RegressTest.cpp:431:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(diffCmd.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function ‘bool RegressTest::startMemoryProfile(bool)’: RegressTest.cpp:573:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ RegressTest.cpp: In member function ‘bool RegressTest::calcMemoryStats()’: RegressTest.cpp:622:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sLine, 4192, fp); ~~~~~^~~~~~~~~~~~~~~~~ compiling regressTestMain.cpp g++ -c -o ../../obj//regressTestMain.o regressTestMain.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/bedtools-2.27.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr -Isrc/utils/ToolBase -Isrc/utils/driver -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../utils//bedFile/ -I../utils//Contexts/ -I../utils//GenomeFile/ -I../utils//lineFileUtilities/ -I../utils//gzstream/ -I../utils//fileType/ -I../utils//general/ -I../utils//BamTools/include -I../utils//BamTools/src -I../utils//version/ -I../utils//FileRecordTools/ -I../utils//FileRecordTools/FileReaders -I../utils//FileRecordTools/Records -I../utils//KeyListOps/ -I../utils//general - Building main bedtools binary. done. - Creating executables for old CLI. done. mkdir -p /<>/bedtools-2.27.1+dfsg/debian/tmp/usr/local/bin for file in bin/* ; do \ cp -f $file /<>/bedtools-2.27.1+dfsg/debian/tmp/usr/local/bin; \ done make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' rm -f debian/bedtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' dh_install install -d debian/bedtools//usr/share/bash-completion/completions cp --reflink=auto -a ./debian/bash_completion/bedtools debian/bedtools//usr/share/bash-completion/completions/ install -d debian/bedtools/usr/bin cp --reflink=auto -a ./bin/annotateBed ./bin/bamToBed ./bin/bamToFastq ./bin/bed12ToBed6 ./bin/bedToBam ./bin/bedToIgv ./bin/bedpeToBam ./bin/bedtools ./bin/closestBed ./bin/clusterBed ./bin/complementBed ./bin/coverageBed ./bin/expandCols ./bin/fastaFromBed ./bin/flankBed ./bin/genomeCoverageBed ./bin/getOverlap ./bin/groupBy ./bin/intersectBed ./bin/linksBed ./bin/mapBed ./bin/maskFastaFromBed ./bin/mergeBed ./bin/multiBamCov ./bin/multiIntersectBed ./bin/nucBed ./bin/pairToBed ./bin/pairToPair ./bin/randomBed ./bin/shiftBed ./bin/shuffleBed ./bin/slopBed ./bin/sortBed ./bin/subtractBed ./bin/tagBam ./bin/unionBedGraphs ./bin/windowBed ./bin/windowMaker debian/bedtools/usr/bin/ install -d debian/bedtools/usr/share/bedtools cp --reflink=auto -a ./genomes debian/bedtools/usr/share/bedtools/ install -d debian/.debhelper/generated/bedtools install -d debian/.debhelper/generated/bedtools-test # make sure all *.sh files are featuring a '#!/bin/bash' as first line # since there are at least two files (test/intersect/{new_test-intersect.sh,performanceTest.sh} # requiring bash this is taken for all scripts instead of checking first via /bin/sh -n for sh in `find /<>/bedtools-2.27.1+dfsg/debian -name "*.sh"` ; do \ if ! head -n1 ${sh} | grep -q '^#! */bin/[ba]*sh' ; then \ sed -i '1 i #!/bin/bash' ${sh} ; \ fi ; \ done make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' dh_installdocs -a install -d debian/bedtools/usr/share/doc/bedtools cp --reflink=auto -a ./README.md debian/bedtools/usr/share/doc/bedtools cp --reflink=auto -a ./debian/README.test debian/bedtools/usr/share/doc/bedtools cp --reflink=auto -a ./debian/tests/run-unit-test debian/bedtools/usr/share/doc/bedtools chown -R 0:0 debian/bedtools/usr/share/doc chmod -R u\+rw,go=rX debian/bedtools/usr/share/doc install -p -m0644 debian/copyright debian/bedtools/usr/share/doc/bedtools/copyright rm -f debian/bedtools.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' dh_installchangelogs RELEASE_HISTORY install -p -m0644 debian/changelog debian/bedtools/usr/share/doc/bedtools/changelog.Debian install -p -m0644 RELEASE_HISTORY debian/bedtools/usr/share/doc/bedtools/changelog make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a cd debian/bedtools chmod a-x usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian gzip -9nf usr/share/doc/bedtools/changelog usr/share/doc/bedtools/changelog.Debian cd '/<>/bedtools-2.27.1+dfsg' rm -f debian/bedtools.debhelper.log debian/rules override_dh_fixperms-arch make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' dh_fixperms find debian/bedtools -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/bedtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/bedtools/usr/share/doc -type f -a -true -a ! -regex 'debian/bedtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/bedtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/bedtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/bedtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x chmod -x /<>/bedtools-2.27.1+dfsg/debian/bedtools/usr/share/bedtools/genomes/*.genome find /<>/bedtools-2.27.1+dfsg/debian -name "*.bed" -executable -exec chmod -x \{\} \; find /<>/bedtools-2.27.1+dfsg/debian -name "*.sh" -not -executable -exec chmod +x \{\} \; make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' dh_missing -a dh_strip -a install -d debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/52 objcopy --only-keep-debug --compress-debug-sections debian/bedtools/usr/bin/bedtools debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/52/29056ab2d79c8439f111e333e9eb163c941359.debug chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/52/29056ab2d79c8439f111e333e9eb163c941359.debug chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/52/29056ab2d79c8439f111e333e9eb163c941359.debug strip --remove-section=.comment --remove-section=.note debian/bedtools/usr/bin/bedtools objcopy --add-gnu-debuglink debian/.debhelper/bedtools/dbgsym-root/usr/lib/debug/.build-id/52/29056ab2d79c8439f111e333e9eb163c941359.debug debian/bedtools/usr/bin/bedtools install -d debian/.debhelper/bedtools/dbgsym-root/usr/share/doc ln -s bedtools debian/.debhelper/bedtools/dbgsym-root/usr/share/doc/bedtools-dbgsym dh_makeshlibs -a rm -f debian/bedtools/DEBIAN/shlibs dh_shlibdeps -a install -d debian/bedtools/DEBIAN dpkg-shlibdeps -Tdebian/bedtools.substvars debian/bedtools/usr/bin/bedtools dh_installdeb -a dh_gencontrol -a echo misc:Depends= >> debian/bedtools.substvars echo misc:Pre-Depends= >> debian/bedtools.substvars install -d debian/.debhelper/bedtools/dbgsym-root/DEBIAN dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/.debhelper/bedtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=bedtools-dbgsym "-DDepends=bedtools (= \${binary:Version})" "-DDescription=debug symbols for bedtools" -DBuild-Ids=5229056ab2d79c8439f111e333e9eb163c941359 -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -pbedtools -ldebian/changelog -Tdebian/bedtools.substvars -Pdebian/bedtools -UMulti-Arch chmod 0644 -- debian/bedtools/DEBIAN/control chown 0:0 -- debian/bedtools/DEBIAN/control dh_md5sums -a cd debian/bedtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/bedtools/DEBIAN/md5sums chown 0:0 -- debian/bedtools/DEBIAN/md5sums cd debian/.debhelper/bedtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/bedtools/dbgsym-root/DEBIAN/md5sums dh_builddeb -a dpkg-deb --build debian/bedtools .. install -d debian/.debhelper/scratch-space/build-bedtools dpkg-deb --build debian/.debhelper/bedtools/dbgsym-root debian/.debhelper/scratch-space/build-bedtools INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing bedtools (in debian/bedtools); do_strip: , oemstrip: pkgstriptranslations: processing bedtools-dbgsym (in debian/.debhelper/bedtools/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/bedtools/DEBIAN/control, package bedtools, directory debian/bedtools .. removing usr/share/doc/bedtools/changelog.gz pkgstripfiles: processing control file: debian/.debhelper/bedtools/dbgsym-root/DEBIAN/control, package bedtools-dbgsym, directory debian/.debhelper/bedtools/dbgsym-root dpkg-deb: building package 'bedtools-dbgsym' in 'debian/.debhelper/scratch-space/build-bedtools/bedtools-dbgsym_2.27.1+dfsg-3_i386.deb'. pkgstripfiles: Truncating usr/share/doc/bedtools/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package bedtools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'bedtools' in '../bedtools_2.27.1+dfsg-3_i386.deb'. Renaming bedtools-dbgsym_2.27.1+dfsg-3_i386.deb to bedtools-dbgsym_2.27.1+dfsg-3_i386.ddeb mv debian/.debhelper/scratch-space/build-bedtools/bedtools-dbgsym_2.27.1\+dfsg-3_i386.deb ../bedtools-dbgsym_2.27.1\+dfsg-3_i386.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../bedtools_2.27.1+dfsg-3_i386.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-source: info: using options from bedtools-2.27.1+dfsg/debian/source/options: --single-debian-patch dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20190207-1715 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bedtools_2.27.1+dfsg-3_i386.changes: ------------------------------------ Format: 1.8 Date: Mon, 04 Feb 2019 05:33:48 -0800 Source: bedtools Binary: bedtools bedtools-test Architecture: i386 Version: 2.27.1+dfsg-3 Distribution: disco-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Michael R. Crusoe Description: bedtools - suite of utilities for comparing genomic features bedtools-test - test data for the bedtools package Closes: 890116 Changes: bedtools (2.27.1+dfsg-3) unstable; urgency=medium . * Team upload. * Print compilation commands * For *i386: use -ffloat-store; disable shuffle tests. Closes: #890116 * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target * Remove trailing whitespace in debian/changelog * Remove trailing whitespace in debian/copyright * mark bedtools-test as Multi-Arch: foreign Checksums-Sha1: a335d346b32c70357ad579417a1a7d241a8a15c9 15516596 bedtools-dbgsym_2.27.1+dfsg-3_i386.ddeb 350757b7cf872bac60773f339f38ead53fa142e7 6593 bedtools_2.27.1+dfsg-3_i386.buildinfo a87b8d4a4c89e88990b3612557da73dc25139999 635808 bedtools_2.27.1+dfsg-3_i386.deb Checksums-Sha256: db6a5853292963b5ef94b78c0ef048721ed8666c7bd3b912d9110f77e9ffa897 15516596 bedtools-dbgsym_2.27.1+dfsg-3_i386.ddeb b38c7b85220607301dbb4836be02bdb358c62ed17b37f72cbdc0537507c9ecce 6593 bedtools_2.27.1+dfsg-3_i386.buildinfo 3265f5dcb70bc242528469af7ac5b9f95a39eccdf360b40483fd8b124c7acaac 635808 bedtools_2.27.1+dfsg-3_i386.deb Files: 27e3616f55685442ae9ea7c9fe92332f 15516596 debug optional bedtools-dbgsym_2.27.1+dfsg-3_i386.ddeb d38b1946405e460792d6a60873edca3d 6593 science optional bedtools_2.27.1+dfsg-3_i386.buildinfo bc1a9fefe681c507ee4f38728c1fdb26 635808 science optional bedtools_2.27.1+dfsg-3_i386.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bedtools_2.27.1+dfsg-3_i386.deb ------------------------------- new debian package, version 2.0. size 635808 bytes: control archive=2192 bytes. 949 bytes, 21 lines control 2915 bytes, 50 lines md5sums Package: bedtools Version: 2.27.1+dfsg-3 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2198 Depends: libc6 (>= 2.23), libgcc1 (>= 1:4.2), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3) Conflicts: filo Replaces: filo Provides: filo Section: science Priority: optional Homepage: https://github.com/arq5x/bedtools2 Description: suite of utilities for comparing genomic features The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by streaming several BEDTools together. . The groupBy utility is distributed in the filo package. drwxr-xr-x root/root 0 2019-02-04 13:33 ./ drwxr-xr-x root/root 0 2019-02-04 13:33 ./usr/ drwxr-xr-x root/root 0 2019-02-04 13:33 ./usr/bin/ -rwxr-xr-x root/root 41 2019-02-04 13:33 ./usr/bin/annotateBed -rwxr-xr-x root/root 41 2019-02-04 13:33 ./usr/bin/bamToBed -rwxr-xr-x root/root 43 2019-02-04 13:33 ./usr/bin/bamToFastq -rwxr-xr-x root/root 44 2019-02-04 13:33 ./usr/bin/bed12ToBed6 -rwxr-xr-x root/root 41 2019-02-04 13:33 ./usr/bin/bedToBam -rwxr-xr-x root/root 36 2019-02-04 13:33 ./usr/bin/bedToIgv -rwxr-xr-x root/root 43 2019-02-04 13:33 ./usr/bin/bedpeToBam -rwxr-xr-x root/root 2147960 2019-02-04 13:33 ./usr/bin/bedtools -rwxr-xr-x root/root 40 2019-02-04 13:33 ./usr/bin/closestBed -rwxr-xr-x root/root 40 2019-02-04 13:33 ./usr/bin/clusterBed -rwxr-xr-x root/root 43 2019-02-04 13:33 ./usr/bin/complementBed -rwxr-xr-x root/root 41 2019-02-04 13:33 ./usr/bin/coverageBed -rwxr-xr-x root/root 39 2019-02-04 13:33 ./usr/bin/expandCols -rwxr-xr-x root/root 41 2019-02-04 13:33 ./usr/bin/fastaFromBed -rwxr-xr-x root/root 38 2019-02-04 13:33 ./usr/bin/flankBed -rwxr-xr-x root/root 42 2019-02-04 13:33 ./usr/bin/genomeCoverageBed -rwxr-xr-x root/root 40 2019-02-04 13:33 ./usr/bin/getOverlap -rwxr-xr-x root/root 40 2019-02-04 13:33 ./usr/bin/groupBy -rwxr-xr-x root/root 42 2019-02-04 13:33 ./usr/bin/intersectBed -rwxr-xr-x root/root 38 2019-02-04 13:33 ./usr/bin/linksBed -rwxr-xr-x root/root 36 2019-02-04 13:33 ./usr/bin/mapBed -rwxr-xr-x root/root 42 2019-02-04 13:33 ./usr/bin/maskFastaFromBed -rwxr-xr-x root/root 38 2019-02-04 13:33 ./usr/bin/mergeBed -rwxr-xr-x root/root 41 2019-02-04 13:33 ./usr/bin/multiBamCov -rwxr-xr-x root/root 43 2019-02-04 13:33 ./usr/bin/multiIntersectBed -rwxr-xr-x root/root 36 2019-02-04 13:33 ./usr/bin/nucBed -rwxr-xr-x root/root 42 2019-02-04 13:33 ./usr/bin/pairToBed -rwxr-xr-x root/root 43 2019-02-04 13:33 ./usr/bin/pairToPair -rwxr-xr-x root/root 39 2019-02-04 13:33 ./usr/bin/randomBed -rwxr-xr-x root/root 38 2019-02-04 13:33 ./usr/bin/shiftBed -rwxr-xr-x root/root 40 2019-02-04 13:33 ./usr/bin/shuffleBed -rwxr-xr-x root/root 37 2019-02-04 13:33 ./usr/bin/slopBed -rwxr-xr-x root/root 37 2019-02-04 13:33 ./usr/bin/sortBed -rwxr-xr-x root/root 41 2019-02-04 13:33 ./usr/bin/subtractBed -rwxr-xr-x root/root 36 2019-02-04 13:33 ./usr/bin/tagBam -rwxr-xr-x root/root 42 2019-02-04 13:33 ./usr/bin/unionBedGraphs -rwxr-xr-x root/root 39 2019-02-04 13:33 ./usr/bin/windowBed -rwxr-xr-x root/root 44 2019-02-04 13:33 ./usr/bin/windowMaker drwxr-xr-x root/root 0 2019-02-04 13:33 ./usr/share/ drwxr-xr-x root/root 0 2019-02-04 13:33 ./usr/share/bash-completion/ drwxr-xr-x root/root 0 2019-02-04 13:33 ./usr/share/bash-completion/completions/ -rw-r--r-- root/root 638 2019-02-04 13:33 ./usr/share/bash-completion/completions/bedtools drwxr-xr-x root/root 0 2019-02-04 13:33 ./usr/share/bedtools/ drwxr-xr-x root/root 0 2017-12-14 17:15 ./usr/share/bedtools/genomes/ -rw-r--r-- root/root 868 2017-12-14 17:15 ./usr/share/bedtools/genomes/human.hg18.genome -rw-r--r-- root/root 1984 2017-12-14 17:15 ./usr/share/bedtools/genomes/human.hg19.genome -rw-r--r-- root/root 11684 2017-12-14 17:15 ./usr/share/bedtools/genomes/human.hg38.genome -rw-r--r-- root/root 1417 2017-12-14 17:15 ./usr/share/bedtools/genomes/mouse.mm10.genome -rw-r--r-- root/root 577 2017-12-14 17:15 ./usr/share/bedtools/genomes/mouse.mm8.genome -rw-r--r-- root/root 596 2017-12-14 17:15 ./usr/share/bedtools/genomes/mouse.mm9.genome drwxr-xr-x root/root 0 2019-02-04 13:33 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-02-04 13:33 ./usr/share/doc/bedtools/ -rw-r--r-- root/root 3244 2017-12-14 17:15 ./usr/share/doc/bedtools/README.md -rw-r--r-- root/root 278 2019-02-04 13:33 ./usr/share/doc/bedtools/README.test -rw-r--r-- root/root 1695 2019-02-04 13:33 ./usr/share/doc/bedtools/changelog.Debian.gz -rw-r--r-- root/root 5341 2019-02-04 13:33 ./usr/share/doc/bedtools/copyright -rw-r--r-- root/root 398 2019-02-04 13:33 ./usr/share/doc/bedtools/run-unit-test +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: i386 Build-Space: 308916 Build-Time: 169 Distribution: disco-proposed Host Architecture: i386 Install-Time: 19 Job: bedtools_2.27.1+dfsg-3.dsc Machine Architecture: amd64 Package: bedtools Package-Time: 191 Source-Version: 2.27.1+dfsg-3 Space: 308916 Status: successful Version: 2.27.1+dfsg-3 -------------------------------------------------------------------------------- Finished at 20190207-1715 Build needed 00:03:11, 308916k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-16364536 Scanning for processes to kill in build PACKAGEBUILD-16364536