https://launchpad.net/ubuntu/+source/bedtools/2.27.1+dfsg-1/+build/14333850 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-arm64-019 4.4.0-119-generic #143-Ubuntu SMP Mon Apr 2 16:10:02 UTC 2018 aarch64 Buildd toolchain package versions: launchpad-buildd_160 python-lpbuildd_160 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_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.4 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 21 Apr 12:25:20 ntpdate[1824]: adjust time server 10.211.37.1 offset 0.000125 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14333850 /home/buildd/filecache-default/b70461af4419c13dbae7acd6fe74d075a1a9550f Creating target for build PACKAGEBUILD-14333850 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14333850 Starting target for build PACKAGEBUILD-14333850 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14333850 'deb http://ftpmaster.internal/ubuntu bionic main universe' 'deb http://ftpmaster.internal/ubuntu bionic-security main universe' 'deb http://ftpmaster.internal/ubuntu bionic-updates main universe' 'deb http://ftpmaster.internal/ubuntu bionic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-14333850 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14333850 Updating target for build PACKAGEBUILD-14333850 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [235 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu bionic-proposed InRelease [235 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main armhf Packages [972 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main Translation-en [517 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/universe armhf Packages [8264 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4941 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf Packages [9104 B] Get:10 http://ftpmaster.internal/ubuntu bionic-proposed/main Translation-en [7712 B] Get:11 http://ftpmaster.internal/ubuntu bionic-proposed/universe armhf Packages [27.6 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-proposed/universe Translation-en [20.0 kB] Fetched 15.4 MB in 6s (2501 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: gnupg-agent libcryptsetup4 libcurl3-gnutls libgdbm3 libgssapi-krb5-2 libisl15 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmpfr4 libnghttp2-14 libpsl5 librtmp1 libssl1.0.0 libunistring0 libustr-1.0-1 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: dirmngr gcc-8-base gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpg-wks-server gpgconf gpgsm libargon2-0 libcom-err2 libcryptsetup12 libext2fs2 libgdbm-compat4 libgdbm5 libisl19 libjson-c3 libmpfr6 libnghttp2-14 libssl1.1 libunistring2 libzstd1 The following packages will be upgraded: adduser advancecomp apt apt-transport-https base-files base-passwd bash binutils binutils-arm-linux-gnueabihf binutils-common bsdutils build-essential ca-certificates coreutils cpp cpp-7 dash debconf debianutils dmsetup dpkg dpkg-dev e2fslibs e2fsprogs fakeroot fdisk findutils g++ g++-7 gcc gcc-7 gcc-7-base gnupg gnupg-agent gpgv hostname init init-system-helpers libapparmor1 libapt-pkg5.0 libasan4 libasn1-8-heimdal libassuan0 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcilkrts5 libcomerr2 libcurl3-gnutls libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi6 libgcc-7-dev libgcc1 libgcrypt20 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libidn11 libidn2-0 libip4tc0 libisl15 libk5crypto3 libkeyutils1 libkmod2 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblockfile-bin liblockfile1 liblz4-1 libmount1 libmpc3 libncurses5 libncursesw5 libnettle6 libnpth0 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre3 libperl5.26 libpng16-16 libprocps6 libpsl5 libreadline7 libroken18-heimdal libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-7-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libubsan0 libudev1 libuuid1 libwind0-heimdal linux-libc-dev login lsb-base make mawk mount multiarch-support ncurses-base ncurses-bin openssl optipng passwd patch perl perl-base perl-modules-5.26 pinentry-curses pkgbinarymangler procps readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tzdata ubuntu-keyring util-linux 156 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. Need to get 61.7 MB of archives. After this operation, 6660 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic/main armhf base-files armhf 10.1ubuntu1 [58.2 kB] Get:2 http://ftpmaster.internal/ubuntu bionic/main armhf debianutils armhf 4.8.4 [84.5 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main armhf bash armhf 4.4.18-2ubuntu1 [552 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main armhf bsdutils armhf 1:2.31.1-0.4ubuntu3 [55.2 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main armhf coreutils armhf 8.28-1ubuntu1 [1128 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main armhf perl-modules-5.26 all 5.26.1-6 [2760 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main armhf libgdbm5 armhf 1.14.1-6 [23.4 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main armhf libgdbm-compat4 armhf 1.14.1-6 [5764 B] Get:9 http://ftpmaster.internal/ubuntu bionic/main armhf libperl5.26 armhf 5.26.1-6 [2885 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main armhf perl armhf 5.26.1-6 [201 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main armhf perl-base armhf 5.26.1-6 [1290 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main armhf libc6-dev armhf 2.27-3ubuntu1 [1899 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main armhf libc-dev-bin armhf 2.27-3ubuntu1 [59.4 kB] Get:14 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf linux-libc-dev armhf 4.15.0-18.19 [997 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main armhf libc6 armhf 2.27-3ubuntu1 [2207 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main armhf libc-bin armhf 2.27-3ubuntu1 [464 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main armhf gcc-8-base armhf 8-20180414-1ubuntu2 [18.2 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main armhf libgcc1 armhf 1:8-20180414-1ubuntu2 [37.1 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main armhf libzstd1 armhf 1.3.3+dfsg-2ubuntu1 [168 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main armhf dpkg armhf 1.19.0.5ubuntu2 [1095 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main armhf dash armhf 0.5.8-2.10 [80.4 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main armhf libcom-err2 armhf 1.44.1-1 [9076 B] Get:23 http://ftpmaster.internal/ubuntu bionic/main armhf libcomerr2 armhf 1.44.1-1 [2696 B] Get:24 http://ftpmaster.internal/ubuntu bionic/main armhf libext2fs2 armhf 1.44.1-1 [145 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main armhf e2fslibs armhf 1.44.1-1 [2700 B] Get:26 http://ftpmaster.internal/ubuntu bionic/main armhf e2fsprogs armhf 1.44.1-1 [369 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main armhf findutils armhf 4.6.0+git+20170828-2 [277 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main armhf hostname armhf 3.20 [10.4 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main armhf login armhf 1:4.5-1ubuntu1 [303 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main armhf libncurses5 armhf 6.1-1ubuntu1 [74.8 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main armhf libtinfo5 armhf 6.1-1ubuntu1 [68.4 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main armhf ncurses-bin armhf 6.1-1ubuntu1 [155 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/main armhf libncursesw5 armhf 6.1-1ubuntu1 [95.7 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main armhf sed armhf 4.4-2 [175 kB] Get:35 http://ftpmaster.internal/ubuntu bionic/main armhf libuuid1 armhf 2.31.1-0.4ubuntu3 [19.2 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main armhf libblkid1 armhf 2.31.1-0.4ubuntu3 [112 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main armhf libsmartcols1 armhf 2.31.1-0.4ubuntu3 [74.3 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/main armhf libfdisk1 armhf 2.31.1-0.4ubuntu3 [151 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/main armhf libpcre3 armhf 2:8.39-9 [209 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main armhf libselinux1 armhf 2.7-2build2 [58.9 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main armhf libmount1 armhf 2.31.1-0.4ubuntu3 [122 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main armhf fdisk armhf 2.31.1-0.4ubuntu3 [97.6 kB] Get:43 http://ftpmaster.internal/ubuntu bionic/main armhf util-linux armhf 2.31.1-0.4ubuntu3 [845 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main armhf base-passwd armhf 3.5.44 [45.9 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main armhf init-system-helpers all 1.51 [37.3 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main armhf ncurses-base all 6.1-1ubuntu1 [17.3 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main armhf sysvinit-utils armhf 2.88dsf-59.10ubuntu1 [17.2 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main armhf liblz4-1 armhf 0.0~r131-2ubuntu3 [43.9 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main armhf libstdc++6 armhf 8-20180414-1ubuntu2 [349 kB] Get:50 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libudev1 armhf 237-3ubuntu9 [48.3 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main armhf libapt-pkg5.0 armhf 1.6.1 [728 kB] Get:52 http://ftpmaster.internal/ubuntu bionic/main armhf libaudit-common all 1:2.8.2-1ubuntu1 [4132 B] Get:53 http://ftpmaster.internal/ubuntu bionic/main armhf libcap-ng0 armhf 0.7.7-3.1 [9816 B] Get:54 http://ftpmaster.internal/ubuntu bionic/main armhf libaudit1 armhf 1:2.8.2-1ubuntu1 [35.5 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/main armhf debconf all 1.5.66 [124 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main armhf libpam0g armhf 1.1.8-3.6ubuntu2 [49.5 kB] Get:57 http://ftpmaster.internal/ubuntu bionic/main armhf libsemanage-common all 2.7-2build2 [6904 B] Get:58 http://ftpmaster.internal/ubuntu bionic/main armhf libsemanage1 armhf 2.7-2build2 [72.1 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/main armhf libpam-modules-bin armhf 1.1.8-3.6ubuntu2 [32.4 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main armhf libpam-modules armhf 1.1.8-3.6ubuntu2 [224 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/main armhf passwd armhf 1:4.5-1ubuntu1 [769 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main armhf adduser all 3.116ubuntu1 [163 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main armhf libgpg-error0 armhf 1.27-6 [33.6 kB] Get:64 http://ftpmaster.internal/ubuntu bionic/main armhf libgcrypt20 armhf 1.8.1-4ubuntu1 [364 kB] Get:65 http://ftpmaster.internal/ubuntu bionic/main armhf gpgv armhf 2.2.4-1ubuntu1 [166 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main armhf ubuntu-keyring all 2018.02.28 [20.7 kB] Get:67 http://ftpmaster.internal/ubuntu bionic/main armhf libunistring2 armhf 0.9.9-0ubuntu1 [352 kB] Get:68 http://ftpmaster.internal/ubuntu bionic/main armhf libgmp10 armhf 2:6.1.2+dfsg-2 [182 kB] Get:69 http://ftpmaster.internal/ubuntu bionic/main armhf libnettle6 armhf 3.4-1 [123 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/main armhf libhogweed4 armhf 3.4-1 [127 kB] Get:71 http://ftpmaster.internal/ubuntu bionic/main armhf libidn2-0 armhf 2.0.4-1.1build2 [46.1 kB] Get:72 http://ftpmaster.internal/ubuntu bionic/main armhf libffi6 armhf 3.2.1-8 [16.4 kB] Get:73 http://ftpmaster.internal/ubuntu bionic/main armhf libp11-kit0 armhf 0.23.9-2 [162 kB] Get:74 http://ftpmaster.internal/ubuntu bionic/main armhf libtasn1-6 armhf 4.13-2 [31.1 kB] Get:75 http://ftpmaster.internal/ubuntu bionic/main armhf libgnutls30 armhf 3.5.18-1ubuntu1 [585 kB] Get:76 http://ftpmaster.internal/ubuntu bionic/main armhf libseccomp2 armhf 2.3.1-2.1ubuntu4 [29.8 kB] Get:77 http://ftpmaster.internal/ubuntu bionic/main armhf apt armhf 1.6.1 [1122 kB] Get:78 http://ftpmaster.internal/ubuntu bionic/main armhf libargon2-0 armhf 0~20161029-1.1 [20.4 kB] Get:79 http://ftpmaster.internal/ubuntu bionic/main armhf libjson-c3 armhf 0.12.1-1.3 [19.6 kB] Get:80 http://ftpmaster.internal/ubuntu bionic/main armhf libdevmapper1.02.1 armhf 2:1.02.145-4.1ubuntu3 [117 kB] Get:81 http://ftpmaster.internal/ubuntu bionic/main armhf libcryptsetup12 armhf 2:2.0.2-1ubuntu1 [119 kB] Get:82 http://ftpmaster.internal/ubuntu bionic/main armhf libapparmor1 armhf 2.12-4ubuntu5 [27.3 kB] Get:83 http://ftpmaster.internal/ubuntu bionic/main armhf libcap2 armhf 1:2.25-1.2 [11.7 kB] Get:84 http://ftpmaster.internal/ubuntu bionic/main armhf libidn11 armhf 1.33-2.1ubuntu1 [43.4 kB] Get:85 http://ftpmaster.internal/ubuntu bionic/main armhf libip4tc0 armhf 1.6.1-2ubuntu2 [17.8 kB] Get:86 http://ftpmaster.internal/ubuntu bionic/main armhf libkmod2 armhf 24-1ubuntu3 [34.4 kB] Get:87 http://ftpmaster.internal/ubuntu bionic/main armhf mount armhf 2.31.1-0.4ubuntu3 [99.7 kB] Get:88 http://ftpmaster.internal/ubuntu bionic/main armhf libprocps6 armhf 2:3.3.12-3ubuntu1 [28.4 kB] Get:89 http://ftpmaster.internal/ubuntu bionic/main armhf lsb-base all 9.20170808ubuntu1 [12.5 kB] Get:90 http://ftpmaster.internal/ubuntu bionic/main armhf procps armhf 2:3.3.12-3ubuntu1 [214 kB] Get:91 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf systemd armhf 237-3ubuntu9 [2720 kB] Get:92 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libsystemd0 armhf 237-3ubuntu9 [185 kB] Get:93 http://ftpmaster.internal/ubuntu bionic/main armhf mawk armhf 1.3.3-17ubuntu3 [72.5 kB] Get:94 http://ftpmaster.internal/ubuntu bionic/main armhf init armhf 1.51 [5864 B] Get:95 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf systemd-sysv armhf 237-3ubuntu9 [11.6 kB] Get:96 http://ftpmaster.internal/ubuntu bionic/main armhf libpam-runtime all 1.1.8-3.6ubuntu2 [37.0 kB] Get:97 http://ftpmaster.internal/ubuntu bionic/main armhf libss2 armhf 1.44.1-1 [9380 B] Get:98 http://ftpmaster.internal/ubuntu bionic/main armhf sensible-utils all 0.0.12 [14.8 kB] Get:99 http://ftpmaster.internal/ubuntu bionic/main armhf libssl1.1 armhf 1.1.0g-2ubuntu3 [911 kB] Get:100 http://ftpmaster.internal/ubuntu bionic/main armhf openssl armhf 1.1.0g-2ubuntu3 [510 kB] Get:101 http://ftpmaster.internal/ubuntu bionic/main armhf ca-certificates all 20180409 [151 kB] Get:102 http://ftpmaster.internal/ubuntu bionic/main armhf dmsetup armhf 2:1.02.145-4.1ubuntu3 [73.7 kB] Get:103 http://ftpmaster.internal/ubuntu bionic/main armhf readline-common all 7.0-3 [52.9 kB] Get:104 http://ftpmaster.internal/ubuntu bionic/main armhf libreadline7 armhf 7.0-3 [103 kB] Get:105 http://ftpmaster.internal/ubuntu bionic/main armhf libslang2 armhf 2.3.1a-3ubuntu1 [381 kB] Get:106 http://ftpmaster.internal/ubuntu bionic/main armhf libsqlite3-0 armhf 3.22.0-1 [421 kB] Get:107 http://ftpmaster.internal/ubuntu bionic/main armhf tzdata all 2018d-1 [188 kB] Get:108 http://ftpmaster.internal/ubuntu bionic/main armhf libgssapi-krb5-2 armhf 1.16-2build1 [101 kB] Get:109 http://ftpmaster.internal/ubuntu bionic/main armhf libkrb5-3 armhf 1.16-2build1 [233 kB] Get:110 http://ftpmaster.internal/ubuntu bionic/main armhf libk5crypto3 armhf 1.16-2build1 [83.2 kB] Get:111 http://ftpmaster.internal/ubuntu bionic/main armhf libkrb5support0 armhf 1.16-2build1 [27.5 kB] Get:112 http://ftpmaster.internal/ubuntu bionic/main armhf libkeyutils1 armhf 1.5.9-9.2ubuntu2 [7796 B] Get:113 http://ftpmaster.internal/ubuntu bionic/main armhf libpng16-16 armhf 1.6.34-1 [159 kB] Get:114 http://ftpmaster.internal/ubuntu bionic/main armhf libpsl5 armhf 0.19.1-5build1 [40.5 kB] Get:115 http://ftpmaster.internal/ubuntu bionic/main armhf libssl1.0.0 armhf 1.0.2n-1ubuntu5 [710 kB] Get:116 http://ftpmaster.internal/ubuntu bionic/main armhf multiarch-support armhf 2.27-3ubuntu1 [6912 B] Get:117 http://ftpmaster.internal/ubuntu bionic/main armhf advancecomp armhf 2.1-1 [166 kB] Get:118 http://ftpmaster.internal/ubuntu bionic/universe armhf apt-transport-https all 1.6.1 [1692 B] Get:119 http://ftpmaster.internal/ubuntu bionic/main armhf libbinutils armhf 2.30-15ubuntu1 [309 kB] Get:120 http://ftpmaster.internal/ubuntu bionic/main armhf binutils armhf 2.30-15ubuntu1 [3360 B] Get:121 http://ftpmaster.internal/ubuntu bionic/main armhf binutils-common armhf 2.30-15ubuntu1 [193 kB] Get:122 http://ftpmaster.internal/ubuntu bionic/main armhf binutils-arm-linux-gnueabihf armhf 2.30-15ubuntu1 [2175 kB] Get:123 http://ftpmaster.internal/ubuntu bionic/main armhf libgomp1 armhf 8-20180414-1ubuntu2 [66.6 kB] Get:124 http://ftpmaster.internal/ubuntu bionic/main armhf libatomic1 armhf 8-20180414-1ubuntu2 [7060 B] Get:125 http://ftpmaster.internal/ubuntu bionic/main armhf libasan4 armhf 7.3.0-16ubuntu3 [328 kB] Get:126 http://ftpmaster.internal/ubuntu bionic/main armhf libubsan0 armhf 7.3.0-16ubuntu3 [108 kB] Get:127 http://ftpmaster.internal/ubuntu bionic/main armhf libcilkrts5 armhf 7.3.0-16ubuntu3 [35.9 kB] Get:128 http://ftpmaster.internal/ubuntu bionic/main armhf g++-7 armhf 7.3.0-16ubuntu3 [6049 kB] Get:129 http://ftpmaster.internal/ubuntu bionic/main armhf gcc-7 armhf 7.3.0-16ubuntu3 [5943 kB] Get:130 http://ftpmaster.internal/ubuntu bionic/main armhf libstdc++-7-dev armhf 7.3.0-16ubuntu3 [1535 kB] Get:131 http://ftpmaster.internal/ubuntu bionic/main armhf libgcc-7-dev armhf 7.3.0-16ubuntu3 [708 kB] Get:132 http://ftpmaster.internal/ubuntu bionic/main armhf libcc1-0 armhf 8-20180414-1ubuntu2 [32.7 kB] Get:133 http://ftpmaster.internal/ubuntu bionic/main armhf cpp-7 armhf 7.3.0-16ubuntu3 [5296 kB] Get:134 http://ftpmaster.internal/ubuntu bionic/main armhf gcc-7-base armhf 7.3.0-16ubuntu3 [18.9 kB] Get:135 http://ftpmaster.internal/ubuntu bionic/main armhf libisl19 armhf 0.19-1 [426 kB] Get:136 http://ftpmaster.internal/ubuntu bionic/main armhf libmpc3 armhf 1.1.0-1 [33.2 kB] Get:137 http://ftpmaster.internal/ubuntu bionic/main armhf libmpfr6 armhf 4.0.1-1 [194 kB] Get:138 http://ftpmaster.internal/ubuntu bionic/main armhf cpp armhf 4:7.3.0-3ubuntu2 [27.5 kB] Get:139 http://ftpmaster.internal/ubuntu bionic/main armhf gcc armhf 4:7.3.0-3ubuntu2 [5208 B] Get:140 http://ftpmaster.internal/ubuntu bionic/main armhf g++ armhf 4:7.3.0-3ubuntu2 [1576 B] Get:141 http://ftpmaster.internal/ubuntu bionic/main armhf make armhf 4.1-9.1ubuntu1 [142 kB] Get:142 http://ftpmaster.internal/ubuntu bionic/main armhf dpkg-dev all 1.19.0.5ubuntu2 [607 kB] Get:143 http://ftpmaster.internal/ubuntu bionic/main armhf libdpkg-perl all 1.19.0.5ubuntu2 [211 kB] Get:144 http://ftpmaster.internal/ubuntu bionic/main armhf patch armhf 2.7.6-2ubuntu1 [98.9 kB] Get:145 http://ftpmaster.internal/ubuntu bionic/main armhf build-essential armhf 12.4ubuntu1 [4752 B] Get:146 http://ftpmaster.internal/ubuntu bionic/main armhf gnupg-l10n all 2.2.4-1ubuntu1 [48.6 kB] Get:147 http://ftpmaster.internal/ubuntu bionic/main armhf libassuan0 armhf 2.5.1-2 [28.3 kB] Get:148 http://ftpmaster.internal/ubuntu bionic/main armhf gnupg armhf 2.2.4-1ubuntu1 [249 kB] Get:149 http://ftpmaster.internal/ubuntu bionic/universe armhf gnupg-agent all 2.2.4-1ubuntu1 [4544 B] Get:150 http://ftpmaster.internal/ubuntu bionic/main armhf gpgconf armhf 2.2.4-1ubuntu1 [105 kB] Get:151 http://ftpmaster.internal/ubuntu bionic/main armhf pinentry-curses armhf 1.1.0-1 [31.4 kB] Get:152 http://ftpmaster.internal/ubuntu bionic/main armhf libnpth0 armhf 1.5-3 [6632 B] Get:153 http://ftpmaster.internal/ubuntu bionic/main armhf gpg-agent armhf 2.2.4-1ubuntu1 [189 kB] Get:154 http://ftpmaster.internal/ubuntu bionic/main armhf gnupg-utils armhf 2.2.4-1ubuntu1 [106 kB] Get:155 http://ftpmaster.internal/ubuntu bionic/main armhf gpg armhf 2.2.4-1ubuntu1 [409 kB] Get:156 http://ftpmaster.internal/ubuntu bionic/main armhf gpg-wks-client armhf 2.2.4-1ubuntu1 [76.8 kB] Get:157 http://ftpmaster.internal/ubuntu bionic/main armhf gpg-wks-server armhf 2.2.4-1ubuntu1 [71.8 kB] Get:158 http://ftpmaster.internal/ubuntu bionic/main armhf gpgsm armhf 2.2.4-1ubuntu1 [183 kB] Get:159 http://ftpmaster.internal/ubuntu bionic/main armhf dirmngr armhf 2.2.4-1ubuntu1 [275 kB] Get:160 http://ftpmaster.internal/ubuntu bionic/main armhf libfakeroot armhf 1.22-2ubuntu1 [21.6 kB] Get:161 http://ftpmaster.internal/ubuntu bionic/main armhf fakeroot armhf 1.22-2ubuntu1 [60.3 kB] Get:162 http://ftpmaster.internal/ubuntu bionic/main armhf libroken18-heimdal armhf 7.5.0+dfsg-1 [34.1 kB] Get:163 http://ftpmaster.internal/ubuntu bionic/main armhf libasn1-8-heimdal armhf 7.5.0+dfsg-1 [136 kB] Get:164 http://ftpmaster.internal/ubuntu bionic/main armhf libnghttp2-14 armhf 1.30.0-1ubuntu1 [67.4 kB] Get:165 http://ftpmaster.internal/ubuntu bionic/main armhf libcurl3-gnutls armhf 7.58.0-2ubuntu3 [182 kB] Get:166 http://ftpmaster.internal/ubuntu bionic/main armhf libheimbase1-heimdal armhf 7.5.0+dfsg-1 [24.1 kB] Get:167 http://ftpmaster.internal/ubuntu bionic/main armhf libhcrypto4-heimdal armhf 7.5.0+dfsg-1 [76.5 kB] Get:168 http://ftpmaster.internal/ubuntu bionic/main armhf libwind0-heimdal armhf 7.5.0+dfsg-1 [47.2 kB] Get:169 http://ftpmaster.internal/ubuntu bionic/main armhf libhx509-5-heimdal armhf 7.5.0+dfsg-1 [87.9 kB] Get:170 http://ftpmaster.internal/ubuntu bionic/main armhf libkrb5-26-heimdal armhf 7.5.0+dfsg-1 [168 kB] Get:171 http://ftpmaster.internal/ubuntu bionic/main armhf libheimntlm0-heimdal armhf 7.5.0+dfsg-1 [13.1 kB] Get:172 http://ftpmaster.internal/ubuntu bionic/main armhf libgssapi3-heimdal armhf 7.5.0+dfsg-1 [78.8 kB] Get:173 http://ftpmaster.internal/ubuntu bionic/universe armhf libisl15 armhf 0.18-4 [423 kB] Get:174 http://ftpmaster.internal/ubuntu bionic/main armhf liblockfile-bin armhf 1.14-1.1 [10.9 kB] Get:175 http://ftpmaster.internal/ubuntu bionic/main armhf liblockfile1 armhf 1.14-1.1 [5784 B] Get:176 http://ftpmaster.internal/ubuntu bionic/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-3ubuntu2 [13.0 kB] Get:177 http://ftpmaster.internal/ubuntu bionic/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-3ubuntu2 [42.0 kB] Get:178 http://ftpmaster.internal/ubuntu bionic/main armhf optipng armhf 0.7.6-1.1 [80.6 kB] Get:179 http://ftpmaster.internal/ubuntu bionic/main armhf pkgbinarymangler all 138 [52.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 61.7 MB in 3s (16.1 MB/s) (Reading database ... 12457 files and directories currently 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Setting up openssl (1.1.0g-2ubuntu3) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libsqlite3-0:armhf (3.22.0-1) ... Setting up dmsetup (2:1.02.145-4.1ubuntu3) ... Setting up libmpc3:armhf (1.1.0-1) ... Setting up libc-dev-bin (2.27-3ubuntu1) ... Setting up libcomerr2:armhf (1.44.1-1) ... Setting up libgdbm-compat4:armhf (1.14.1-6) ... Setting up libkeyutils1:armhf (1.5.9-9.2ubuntu2) ... Setting up ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 8 added, 23 removed; done. Setting up libc6-dev:armhf (2.27-3ubuntu1) ... Setting up libslang2:armhf (2.3.1a-3ubuntu1) ... Setting up libassuan0:armhf (2.5.1-2) ... Setting up libisl19:armhf (0.19-1) ... Setting up libk5crypto3:armhf (1.16-2build1) ... Setting up pkgbinarymangler (138) ... Setting up libwind0-heimdal:armhf (7.5.0+dfsg-1) ... Setting up libasan4:armhf (7.3.0-16ubuntu3) ... Setting up libbinutils:armhf (2.30-15ubuntu1) ... 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Setting up gpg (2.2.4-1ubuntu1) ... Setting up cpp (4:7.3.0-3ubuntu2) ... Setting up gcc-7 (7.3.0-16ubuntu3) ... Setting up g++-7 (7.3.0-16ubuntu3) ... Setting up gpg-agent (2.2.4-1ubuntu1) ... Installing new version of config file /etc/X11/Xsession.d/90gpg-agent ... Setting up gcc (4:7.3.0-3ubuntu2) ... Setting up gpg-wks-server (2.2.4-1ubuntu1) ... Setting up gpg-wks-client (2.2.4-1ubuntu1) ... Setting up libgssapi-krb5-2:armhf (1.16-2build1) ... Setting up perl (5.26.1-6) ... Setting up g++ (4:7.3.0-3ubuntu2) ... Setting up gnupg-agent (2.2.4-1ubuntu1) ... Setting up libgssapi3-heimdal:armhf (7.5.0+dfsg-1) ... Setting up libcurl3-gnutls:armhf (7.58.0-2ubuntu3) ... Setting up gnupg (2.2.4-1ubuntu1) ... Setting up libdpkg-perl (1.19.0.5ubuntu2) ... Setting up dpkg-dev (1.19.0.5ubuntu2) ... Setting up build-essential (12.4ubuntu1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Processing triggers for ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-14333850 armhf bionic-proposed -c chroot:build-PACKAGEBUILD-14333850 --arch=armhf --dist=bionic-proposed --nolog bedtools_2.27.1+dfsg-1.dsc Initiating build PACKAGEBUILD-14333850 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-119-generic #143-Ubuntu SMP Mon Apr 2 16:10:02 UTC 2018 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-019.buildd +==============================================================================+ | bedtools 2.27.1+dfsg-1 (armhf) 21 Apr 2018 12:26 | +==============================================================================+ Package: bedtools Version: 2.27.1+dfsg-1 Source Version: 2.27.1+dfsg-1 Distribution: bionic-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/bedtools-3Ub1rh/bedtools-2.27.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/bedtools-3Ub1rh' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-14333850/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bedtools_2.27.1+dfsg-1.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-Wb1wVI/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-Wb1wVI/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Wb1wVI/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Wb1wVI/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Wb1wVI/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-Wb1wVI/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (125 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 packages were automatically installed and are no longer required: gnupg-agent libcryptsetup4 libcurl3-gnutls libgdbm3 libgssapi-krb5-2 libisl15 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmpfr4 libnghttp2-14 libpsl5 librtmp1 libssl1.0.0 libunistring0 libustr-1.0-1 Use 'apt autoremove' to remove them. 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-Wb1wVI/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 ... 12730 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.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-DGp01C/apt_archive/sbuild-build-depends-bedtools-dummy.deb'. Ign:1 copy:/<>/resolver-DGp01C/apt_archive ./ InRelease Get:2 copy:/<>/resolver-DGp01C/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-DGp01C/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-DGp01C/apt_archive ./ Sources [229 B] Get:5 copy:/<>/resolver-DGp01C/apt_archive ./ Packages [549 B] Fetched 2897 B in 0s (131 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 packages were automatically installed and are no longer required: gnupg-agent libcryptsetup4 libgdbm3 libisl15 libmpfr4 libssl1.0.0 libunistring0 libustr-1.0-1 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libhts2 libicu60 libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal samtools zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl cwltool The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libhts2 libicu60 libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal samtools sbuild-build-depends-bedtools-dummy zlib1g-dev 0 upgraded, 42 newly installed, 1 to remove and 0 not upgraded. Need to get 20.3 MB of archives. After this operation, 74.2 MB of additional disk space will be used. 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Setting up libxml2:armhf (2.9.4+dfsg1-6.1ubuntu1) ... Setting up libmagic-mgc (1:5.32-2) ... Setting up libmagic1:armhf (1:5.32-2) ... Setting up libcroco3:armhf (0.6.12-2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up autotools-dev (20180224.1) ... Setting up bsdmainutils (11.1.2ubuntu1) ... 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 libhts2:armhf (1.7-2) ... Setting up libpython2.7-stdlib:armhf (2.7.15~rc1-1) ... Setting up autopoint (0.19.8.1-6) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.040-1.1~build1) ... Setting up gettext (0.19.8.1-6) ... Setting up python2.7 (2.7.15~rc1-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-2) ... Setting up libpython-stdlib:armhf (2.7.15~rc1-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-3ubuntu2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up samtools (1.7-1) ... Setting up python (2.7.15~rc1-1) ... Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (17) ... Setting up dh-strip-nondeterminism (0.040-1.1~build1) ... Setting up debhelper (11.1.6ubuntu1) ... Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ... (Reading database ... 15499 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-119-generic arm64 (armv7l) Toolchain package versions: binutils_2.30-15ubuntu1 dpkg-dev_1.19.0.5ubuntu2 g++-7_7.3.0-16ubuntu3 gcc-7_7.3.0-16ubuntu3 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.3.0-16ubuntu3 libstdc++6_8-20180414-1ubuntu2 linux-libc-dev_4.15.0-18.19 Package versions: adduser_3.116ubuntu1 advancecomp_2.1-1 apt_1.6.1 apt-transport-https_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1ubuntu1 base-passwd_3.5.44 bash_4.4.18-2ubuntu1 binutils_2.30-15ubuntu1 binutils-arm-linux-gnueabihf_2.30-15ubuntu1 binutils-common_2.30-15ubuntu1 bsdmainutils_11.1.2ubuntu1 bsdutils_1:2.31.1-0.4ubuntu3 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 ca-certificates_20180409 coreutils_8.28-1ubuntu1 cpp_4:7.3.0-3ubuntu2 cpp-7_7.3.0-16ubuntu3 dash_0.5.8-2.10 debconf_1.5.66 debhelper_11.1.6ubuntu1 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.040-1.1~build1 diffutils_1:3.6-1 dirmngr_2.2.4-1ubuntu1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu2 dpkg-dev_1.19.0.5ubuntu2 e2fslibs_1.44.1-1 e2fsprogs_1.44.1-1 fakeroot_1.22-2ubuntu1 fdisk_2.31.1-0.4ubuntu3 file_1:5.32-2 findutils_4.6.0+git+20170828-2 g++_4:7.3.0-3ubuntu2 g++-7_7.3.0-16ubuntu3 gcc_4:7.3.0-3ubuntu2 gcc-7_7.3.0-16ubuntu3 gcc-7-base_7.3.0-16ubuntu3 gcc-8-base_8-20180414-1ubuntu2 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gnupg_2.2.4-1ubuntu1 gnupg-agent_2.2.4-1ubuntu1 gnupg-l10n_2.2.4-1ubuntu1 gnupg-utils_2.2.4-1ubuntu1 gpg_2.2.4-1ubuntu1 gpg-agent_2.2.4-1ubuntu1 gpg-wks-client_2.2.4-1ubuntu1 gpg-wks-server_2.2.4-1ubuntu1 gpgconf_2.2.4-1ubuntu1 gpgsm_2.2.4-1ubuntu1 gpgv_2.2.4-1ubuntu1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 hostname_3.20 init_1.51 init-system-helpers_1.51 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu5 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-1.1 libasan4_7.3.0-16ubuntu3 libasn1-8-heimdal_7.5.0+dfsg-1 libassuan0_2.5.1-2 libatomic1_8-20180414-1ubuntu2 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.2-1ubuntu1 libaudit1_1:2.8.2-1ubuntu1 libbinutils_2.30-15ubuntu1 libblkid1_2.31.1-0.4ubuntu3 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3ubuntu1 libc-dev-bin_2.27-3ubuntu1 libc6_2.27-3ubuntu1 libc6-dev_2.27-3ubuntu1 libcap-ng0_0.7.7-3.1 libcap2_1:2.25-1.2 libcc1-0_8-20180414-1ubuntu2 libcilkrts5_7.3.0-16ubuntu3 libcom-err2_1.44.1-1 libcomerr2_1.44.1-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1ubuntu1 libcryptsetup4_2:1.7.3-4ubuntu1 libcurl3-gnutls_7.58.0-2ubuntu3 libdb5.3_5.3.28-13.1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu3 libdpkg-perl_1.19.0.5ubuntu2 libexpat1_2.2.5-3 libext2fs2_1.44.1-1 libfakeroot_1.22-2ubuntu1 libfdisk1_2.31.1-0.4ubuntu3 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1.1~build1 libgcc-7-dev_7.3.0-16ubuntu3 libgcc1_1:8-20180414-1ubuntu2 libgcrypt20_1.8.1-4ubuntu1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2ubuntu1 libgmp10_2:6.1.2+dfsg-2 libgnutls30_3.5.18-1ubuntu1 libgomp1_8-20180414-1ubuntu2 libgpg-error0_1.27-6 libgssapi-krb5-2_1.16-2build1 libgssapi3-heimdal_7.5.0+dfsg-1 libhcrypto4-heimdal_7.5.0+dfsg-1 libheimbase1-heimdal_7.5.0+dfsg-1 libheimntlm0-heimdal_7.5.0+dfsg-1 libhogweed4_3.4-1 libhts2_1.7-2 libhx509-5-heimdal_7.5.0+dfsg-1 libicu60_60.2-3ubuntu3 libidn11_1.33-2.1ubuntu1 libidn2-0_2.0.4-1.1build2 libip4tc0_1.6.1-2ubuntu2 libisl15_0.18-4 libisl19_0.19-1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2build1 libkeyutils1_1.5.9-9.2ubuntu2 libkmod2_24-1ubuntu3 libkrb5-26-heimdal_7.5.0+dfsg-1 libkrb5-3_1.16-2build1 libkrb5support0_1.16-2build1 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1ubuntu1 libldap-common_2.4.45+dfsg-1ubuntu1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblz4-1_0.0~r131-2ubuntu3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-2 libmagic1_1:5.32-2 libmount1_2.31.1-0.4ubuntu3 libmpc3_1.1.0-1 libmpfr4_3.1.6-1 libmpfr6_4.0.1-1 libncurses5_6.1-1ubuntu1 libncursesw5_6.1-1ubuntu1 libnettle6_3.4-1 libnghttp2-14_1.30.0-1ubuntu1 libnpth0_1.5-3 libp11-kit0_0.23.9-2 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_2:8.39-9 libperl5.26_5.26.1-6 libpipeline1_1.5.0-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3ubuntu1 libpsl5_0.19.1-5build1 libpython-stdlib_2.7.15~rc1-1 libpython2.7-minimal_2.7.15~rc1-1 libpython2.7-stdlib_2.7.15~rc1-1 libreadline7_7.0-3 libroken18-heimdal_7.5.0+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.1-2.1ubuntu4 libselinux1_2.7-2build2 libsemanage-common_2.7-2build2 libsemanage1_2.7-2build2 libsepol1_2.7-1 libsigsegv2_2.12-1 libslang2_2.3.1a-3ubuntu1 libsmartcols1_2.31.1-0.4ubuntu3 libsqlite3-0_3.22.0-1 libss2_1.44.1-1 libssl1.0.0_1.0.2n-1ubuntu5 libssl1.1_1.1.0g-2ubuntu3 libstdc++-7-dev_7.3.0-16ubuntu3 libstdc++6_8-20180414-1ubuntu2 libsystemd0_237-3ubuntu9 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1-1ubuntu1 libtool_2.4.6-2 libubsan0_7.3.0-16ubuntu3 libudev1_237-3ubuntu9 libunistring0_0.9.3-5.2ubuntu1 libunistring2_0.9.9-0ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.4ubuntu3 libwind0-heimdal_7.5.0+dfsg-1 libxml2_2.9.4+dfsg1-6.1ubuntu1 libzstd1_1.3.3+dfsg-2ubuntu1 linux-libc-dev_4.15.0-18.19 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.1-9.1ubuntu1 man-db_2.8.3-2 mawk_1.3.3-17ubuntu3 mime-support_3.60ubuntu1 mount_2.31.1-0.4ubuntu3 multiarch-support_2.27-3ubuntu1 ncurses-base_6.1-1ubuntu1 ncurses-bin_6.1-1ubuntu1 openssl_1.1.0g-2ubuntu3 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-2ubuntu1 perl_5.26.1-6 perl-base_5.26.1-6 perl-modules-5.26_5.26.1-6 pinentry-curses_1.1.0-1 pkgbinarymangler_138 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-3ubuntu1 python_2.7.15~rc1-1 python-minimal_2.7.15~rc1-1 python2.7_2.7.15~rc1-1 python2.7-minimal_2.7.15~rc1-1 readline-common_7.0-3 samtools_1.7-1 sbuild-build-depends-bedtools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_237-3ubuntu9 systemd-sysv_237-3ubuntu9 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.29b-2 tzdata_2018d-1 ubuntu-keyring_2018.02.28 util-linux_2.31.1-0.4ubuntu3 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Feb 10 09:59:04 2018 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-1.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-1.debian.tar.xz 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 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-14333850 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-14333850 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-14333850 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-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build bedtools-2.27.1+dfsg dpkg-buildpackage: info: host architecture armhf 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 -O clean * Cleaning-up BamTools API make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' * 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 -O "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' $CXXFLAGS is [-Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -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: ========================================================= make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' DETECTED_VERSION = v2.27.1 CURRENT_VERSION = Updating version file. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * Creating BamTools API make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/FileRecordTools make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/FileRecordTools/FileReaders make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/FileRecordTools/Records make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/bedFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling FileReader.cpp * compiling Record.cpp * compiling EmptyRecord.cpp * compiling SingleLineDelimTextFileReader.cpp * compiling FileRecordMgr.cpp * compiling FileRecordMergeMgr.cpp * compiling Bed3Interval.cpp * compiling BamFileReader.cpp * compiling Bed4Interval.cpp * compiling BufferedStreamMgr.cpp * compiling FileRecordMgr.cpp * compiling FileRecordMergeMgr.cpp - Building in FileReaders * compiling BedGraphInterval.cpp * compiling bedFile.cpp In file included from /usr/include/c++/7/vector:69:0, from ../../utils//lineFileUtilities/lineFileUtilities.h:4, from bedFile.h:17, from bedFile.cpp:12: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from ../../utils//lineFileUtilities/lineFileUtilities.h:4, from bedFile.h:17, from bedFile.cpp:12: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void BedFile::loadBedFileIntoVector()’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from bedFile.h:29, from bedFile.cpp:12: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_algo.h:1880:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __final_insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1880:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from bedFile.h:29, from bedFile.cpp:12: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = BED; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~~~ /usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~~ /usr/include/c++/7/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/algorithm:62:0, from bedFile.h:29, from bedFile.cpp:12: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from bedFile.h:29, from bedFile.cpp:12: /usr/include/c++/7/bits/stl_heap.h:408:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__pop_heap(__first, __last, __last, __comp); ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from bedFile.h:29, from bedFile.cpp:12: /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1672:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__make_heap(__first, __middle, __comp); ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In member function ‘void BedFile::assignWeightsBasedOnSize()’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1971:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from ../../utils//lineFileUtilities/lineFileUtilities.h:4, from bedFile.h:17, from bedFile.cpp:12: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void BedFile::loadBedFileIntoMapNoBin()’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from bedFile.h:29, from bedFile.cpp:12: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1971:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from ../../utils//lineFileUtilities/lineFileUtilities.h:4, from bedFile.h:17, from bedFile.cpp:12: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void BedFile::allHits(std::__cxx11::string, CHRPOS, CHRPOS, std::__cxx11::string, std::vector&, bool, bool, float, bool)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h: In member function ‘void BedFile::addBEDIntoMap(BED)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BinTree make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling InputStreamMgr.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/version make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling version.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/bedGraphFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling InputStreamMgr.cpp - Building in Records * compiling Bed5Interval.cpp * compiling bedGraphFile.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/chromsweep make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling Bed5Interval.cpp * compiling BinTree.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/Contexts make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling Bed6Interval.cpp * compiling Bed6Interval.cpp * compiling PlusFields.cpp * compiling PlusFields.cpp * compiling chromsweep.cpp In file included from /usr/include/c++/7/vector:69:0, from ../../utils//lineFileUtilities/lineFileUtilities.h:4, from chromsweep.cpp:12: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from ../../utils//lineFileUtilities/lineFileUtilities.h:4, from chromsweep.cpp:12: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void ChromSweep::ScanCache()’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h: In member function ‘bool ChromSweep::Next(std::pair >&)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/general make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BedPlusInterval.cpp * compiling BedPlusInterval.cpp * compiling ParseTools.cpp * compiling ContextBase.cpp * compiling Bed12Interval.cpp * compiling PushBackStreamBuf.cpp * compiling CompressionTools.cpp * compiling Bed12Interval.cpp * compiling ContextIntersect.cpp * compiling BamRecord.cpp * compiling Tokenizer.cpp * compiling BamRecord.cpp * compiling ContextFisher.cpp * compiling CommonHelp.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/gzstream make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling GffRecord.cpp g++ -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta -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. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/fileType make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling ContextMap.cpp * compiling GffRecord.cpp * compiling fileType.cpp * compiling GffPlusRecord.cpp * compiling ContextSample.cpp * compiling GffPlusRecord.cpp * compiling VcfRecord.cpp * compiling ContextSpacing.cpp * compiling FileRecordTypeChecker.cpp FileRecordTypeChecker.cpp: In member function ‘bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)’: FileRecordTypeChecker.cpp:365:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int j=0; j < len; j++) { ~~^~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/bedFilePE make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling NoPosPlusRecord.cpp * compiling VcfRecord.cpp * compiling BlockMgr.cpp * compiling NoPosPlusRecord.cpp * compiling ContextMerge.cpp * compiling StrandQueue.cpp * compiling BlockMgr.cpp * compiling ContextJaccard.cpp * compiling bedFilePE.cpp In file included from /usr/include/c++/7/vector:69:0, from bedFilePE.h:4, from bedFilePE.cpp:15: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MATE&}; _Tp = MATE; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from bedFilePE.h:4, from bedFilePE.cpp:15: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void BedFilePE::FindOverlapsPerBin(int, std::__cxx11::string, CHRPOS, CHRPOS, std::__cxx11::string, std::__cxx11::string, std::vector&, float, bool, bool)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h: In member function ‘void BedFilePE::loadBedPEFileIntoMap()’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/KeyListOps make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling StrandQueue.cpp * compiling ContextClosest.cpp * compiling ContextSubtract.cpp * compiling KeyListOps.cpp * compiling RecordMgr.cpp * compiling ContextCoverage.cpp * compiling RecordList.cpp * compiling RecordMgr.cpp * compiling RecordKeyList.cpp * compiling ContextComplement.cpp * compiling RecordList.cpp * compiling KeyListOpsMethods.cpp In file included from /usr/include/c++/7/algorithm:62:0, from ../../utils//fileType/FileRecordTypeChecker.h:18, from ../../utils//FileRecordTools/Records/Record.h:14, from ../../utils//FileRecordTools/Records/RecordKeyVector.h:12, from KeyListOpsMethods.h:15, from KeyListOpsMethods.cpp:8: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from ../../utils//fileType/FileRecordTypeChecker.h:18, from ../../utils//FileRecordTools/Records/Record.h:14, from ../../utils//FileRecordTools/Records/RecordKeyVector.h:12, from KeyListOpsMethods.h:15, from KeyListOpsMethods.cpp:8: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from ../../utils//fileType/FileRecordTypeChecker.h:18, from ../../utils//FileRecordTools/Records/Record.h:14, from ../../utils//FileRecordTools/Records/RecordKeyVector.h:12, from KeyListOpsMethods.h:15, from KeyListOpsMethods.cpp:8: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from ../../utils//fileType/FileRecordTypeChecker.h:18, from ../../utils//FileRecordTools/Records/Record.h:14, from ../../utils//FileRecordTools/Records/RecordKeyVector.h:12, from KeyListOpsMethods.h:15, from KeyListOpsMethods.cpp:8: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from ../../utils//fileType/FileRecordTypeChecker.h:18, from ../../utils//FileRecordTools/Records/Record.h:14, from ../../utils//FileRecordTools/Records/RecordKeyVector.h:12, from KeyListOpsMethods.h:15, from KeyListOpsMethods.cpp:8: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In member function ‘void KeyListOpsMethods::sortArray(bool, bool)’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/NewChromsweep make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling RecordKeyVector.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/sequenceUtilities make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling RecordKeyList.cpp * compiling ContextGroupBy.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/tabFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling sequenceUtils.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BamTools make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling RecordKeyVector.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BamTools-Ancillary make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling tabFile.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BlockedIntervals make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BamAlignment.cpp * compiling NewChromsweep.cpp * compiling BamMultiReader.cpp * compiling BamReader.cpp * compiling BamAncillary.cpp In file included from /usr/include/c++/7/vector:69:0, from ..//lineFileUtilities/lineFileUtilities.h:4, from ..//bedFile/bedFile.h:17, from BamAncillary.h:12, from BamAncillary.cpp:12: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling BlockedIntervals.cpp In file included from /usr/include/c++/7/vector:69:0, from BlockedIntervals.h:12, from BlockedIntervals.cpp:12: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from BlockedIntervals.h:12, from BlockedIntervals.cpp:12: /usr/include/c++/7/bits/stl_vector.h: In function ‘void GetBedBlocks(const BED&, bedVector&)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:69:0, from BlockedIntervals.h:12, from BlockedIntervals.cpp:12: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/Fasta make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BamWriter.cpp * compiling CloseSweep.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/VectorOps make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling SamHeader.cpp * compiling SamProgram.cpp * compiling BamAncillary.cpp In file included from /usr/include/c++/7/vector:69:0, from ..//lineFileUtilities/lineFileUtilities.h:4, from ..//bedFile/bedFile.h:17, from BamAncillary.h:12, from BamAncillary.cpp:12: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BED}; _Tp = BED; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/GenomeFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling Fasta.cpp 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); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:69:0, from Fasta.h:15, from Fasta.cpp:9: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const FastaIndexEntry&}; _Tp = FastaIndexEntry; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/map:60:0, from Fasta.h:12, from Fasta.cpp:9: /usr/include/c++/7/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, FastaIndexEntry>; _KeyOfValue = std::_Select1st, FastaIndexEntry> >; _Compare = std::less >; _Alloc = std::allocator, FastaIndexEntry> >]’: /usr/include/c++/7/bits/stl_tree.h:2395:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, FastaIndexEntry>, std::_Select1st, FastaIndexEntry> >, std::less >, std::allocator, FastaIndexEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator, FastaIndexEntry> >}’ changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/map:61:0, from Fasta.h:12, from Fasta.cpp:9: /usr/include/c++/7/bits/stl_map.h: In member function ‘std::__cxx11::string FastaReference::sequenceNameStartingWith(std::__cxx11::string)’: /usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, FastaIndexEntry>, std::_Select1st, FastaIndexEntry> >, std::less >, std::allocator, FastaIndexEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator, FastaIndexEntry> >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ In file included from /usr/include/c++/7/algorithm:62:0, from Fasta.h:18, from Fasta.cpp:9: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from Fasta.h:18, from Fasta.cpp:9: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = FastaIndexEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_val]’: /usr/include/c++/7/bits/stl_heap.h:128:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __push_heap(_RandomAccessIterator __first, ^~~~~~~~~~~ /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = FastaIndexEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from Fasta.h:18, from Fasta.cpp:9: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/map:61:0, from Fasta.h:12, from Fasta.cpp:9: /usr/include/c++/7/bits/stl_map.h: In function ‘std::ostream& operator<<(std::ostream&, FastaIndex&)’: /usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, FastaIndexEntry>, std::_Select1st, FastaIndexEntry> >, std::less >, std::allocator, FastaIndexEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator, FastaIndexEntry> >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ In file included from /usr/include/c++/7/vector:64:0, from Fasta.h:15, from Fasta.cpp:9: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from Fasta.h:18, from Fasta.cpp:9: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ * compiling SamProgramChain.cpp * compiling split.cpp * compiling SamReadGroup.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/RecordOutputMgr make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling VectorOps.cpp In file included from /usr/include/c++/7/algorithm:62:0, from VectorOps.h:21, from VectorOps.cpp:15: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/vector:69:0, from VectorOps.h:15, from VectorOps.cpp:15: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc: In function ‘_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator*, std::vector > >; _OIter = std::back_insert_iterator >; _UnaryOperation = double (*)(const std::__cxx11::basic_string&)]’: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from VectorOps.h:21, from VectorOps.cpp:15: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from VectorOps.h:21, from VectorOps.cpp:15: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In member function ‘double VectorOps::GetMedian()’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from VectorOps.h:21, from VectorOps.cpp:15: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from VectorOps.h:21, from VectorOps.cpp:15: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from VectorOps.h:21, from VectorOps.cpp:15: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from VectorOps.h:21, from VectorOps.cpp:15: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In member function ‘std::__cxx11::string VectorOps::GetDistinctSortNum(bool)’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/ToolBase make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling SamReadGroupDictionary.cpp * compiling RecordOutputMgr.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/driver make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling SamSequence.cpp * compiling ToolBase.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/annotateBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling GenomeFile.cpp 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 NewGenomeFile.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bamToBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling SamSequenceDictionary.cpp * compiling annotateMain.cpp annotateMain.cpp: In function ‘int annotate_main(int, char**)’: annotateMain.cpp:39:10: warning: variable ‘haveTitles’ set but not used [-Wunused-but-set-variable] bool haveTitles = false; ^~~~~~~~~~ * compiling BedtoolsDriver.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bamToFastq make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BamHeader_p.cpp * compiling bamToFastqMain.cpp 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 bamToBed.cpp 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; ^~~~~~~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bedToBam make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling annotateBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bedpeToBam make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling bamToFastq.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bedToIgv make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BamMultiReader_p.cpp * compiling bedToBam.cpp 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; ^~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bed12ToBed6 make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling bedpeToBam.cpp 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; ^~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/closestFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BamRandomAccessController_p.cpp * compiling bed12ToBed6.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/clusterBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling bedToIgv.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/complementFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling closestHelp.cpp * compiling complementHelp.cpp * compiling clusterMain.cpp 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 make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/coverageFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BamReader_p.cpp * compiling coverageHelp.cpp * compiling complementFile.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/expand make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BamWriter_p.cpp * compiling clusterBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/fastaFromBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BamIndexFactory_p.cpp * compiling coverageFile.cpp 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); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/flankBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling fastaFromBedMain.cpp * compiling expand.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/genomeCoverageBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling flankBedMain.cpp * compiling fastaFromBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/getOverlap make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BamStandardIndex_p.cpp In file included from /usr/include/c++/7/vector:69:0, from src/api/BamAux.h:18, from src/api/BamAlignment.h:14, from src/api/internal/index/BamStandardIndex_p.cpp:10: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BaiAlignmentChunk&}; _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from src/api/BamAux.h:18, from src/api/BamAlignment.h:14, from src/api/internal/index/BamStandardIndex_p.cpp:10: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::SaveAlignmentChunkToBin(BamTools::Internal::BaiBinMap&, const uint32_t&, const uint64_t&, const uint64_t&)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:69:0, from src/api/BamAux.h:18, from src/api/BamAlignment.h:14, from src/api/internal/index/BamStandardIndex_p.cpp:10: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from src/api/BamAux.h:18, from src/api/BamAlignment.h:14, from src/api/internal/index/BamStandardIndex_p.cpp:10: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamStandardIndex::SaveLinearOffsetEntry(BamTools::Internal::BaiLinearOffsetVector&, const int&, const int&, const uint64_t&)’: /usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:69:0, from src/api/BamAux.h:18, from src/api/BamAlignment.h:14, from src/api/internal/index/BamStandardIndex_p.cpp:10: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc: In member function ‘void BamTools::Internal::BamStandardIndex::CalculateCandidateOffsets(const BamTools::Internal::BaiReferenceSummary&, const uint64_t&, std::set&, std::vector&)’: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from src/api/internal/index/BamStandardIndex_p.cpp:21: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from src/api/internal/index/BamStandardIndex_p.cpp:21: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from src/api/internal/index/BamStandardIndex_p.cpp:21: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from src/api/internal/index/BamStandardIndex_p.cpp:21: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from src/api/internal/index/BamStandardIndex_p.cpp:21: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In member function ‘void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ * compiling genomeCoverageMain.cpp * compiling flankBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/groupBy make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling getOverlap.cpp 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; ^~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/intersectFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling intersectHelp.cpp * compiling BamToolsIndex_p.cpp In file included from /usr/include/c++/7/vector:69:0, from src/api/BamAux.h:18, from src/api/BamAlignment.h:14, from src/api/internal/index/BamToolsIndex_p.cpp:10: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BtiBlock&}; _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from src/api/BamAux.h:18, from src/api/BamAlignment.h:14, from src/api/internal/index/BamToolsIndex_p.cpp:10: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void BamTools::Internal::BamToolsIndex::ReadBlocks(const BamTools::Internal::BtiReferenceSummary&, BamTools::Internal::BtiBlockVector&)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:69:0, from src/api/BamAux.h:18, from src/api/BamAlignment.h:14, from src/api/internal/index/BamToolsIndex_p.cpp:10: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BamTools::Internal::BtiReferenceSummary}; _Tp = BamTools::Internal::BtiReferenceSummary; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc: In member function ‘void BamTools::Internal::BamToolsIndex::InitializeFileSummary(const int&)’: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from src/api/BamAux.h:18, from src/api/BamAlignment.h:14, from src/api/internal/index/BamToolsIndex_p.cpp:10: /usr/include/c++/7/bits/stl_vector.h: In member function ‘virtual bool BamTools::Internal::BamToolsIndex::Create()’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ * compiling groupBy.cpp * compiling BamDeviceFactory_p.cpp * compiling genomeCoverageBed.cpp genomeCoverageBed.cpp: In member function ‘void BedGenomeCoverage::CoverageBam(std::__cxx11::string)’: genomeCoverageBed.cpp:322:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(end<_fragmentSize) { //sometimes fragmentSize is bigger :( ~~~^~~~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/fisher make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling intersectFile.cpp 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 BamFile_p.cpp * compiling groupByHelp.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/jaccard make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling fisherHelp.cpp * compiling kfunc.cpp * compiling jaccardHelp.cpp * compiling fisher.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/linksBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BamFtp_p.cpp * compiling BamHttp_p.cpp * compiling jaccard.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/maskFastaFromBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BamPipe_p.cpp * compiling linksMain.cpp * compiling ByteArray_p.cpp * compiling maskFastaFromBedMain.cpp * compiling BgzfStream_p.cpp * compiling HostAddress_p.cpp 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 * compiling linksBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/mapFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling ILocalIODevice_p.cpp * compiling mapHelp.cpp * compiling maskFastaFromBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/mergeFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling RollingBuffer_p.cpp * compiling HttpHeader_p.cpp * compiling mergeHelp.cpp * compiling TcpSocketEngine_p.cpp * compiling mapFile.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/multiBamCov make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling TcpSocketEngine_unix_p.cpp * compiling mergeFile.cpp * compiling TcpSocket_p.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/multiIntersectBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling SamFormatParser_p.cpp * compiling multiBamCovMain.cpp 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 multiIntersectBedMain.cpp 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 SamFormatPrinter_p.cpp * compiling SamHeaderValidator_p.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/nucBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling BamException_p.cpp * 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 make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/pairToBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling multiBamCov.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/pairToPair make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling nucBedMain.cpp * compiling pairToPairMain.cpp 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 pairToBedMain.cpp 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; ^~~~~~~~~~~~ * compiling multiIntersectBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/randomBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling nucBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/regressTest make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling randomBedMain.cpp * compiling pairToPair.cpp 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; ^~~~~~ In file included from /usr/include/c++/7/vector:69:0, from ../utils//lineFileUtilities/lineFileUtilities.h:4, from pairToPair.cpp:12: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MATE&}; _Tp = MATE; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from ../utils//lineFileUtilities/lineFileUtilities.h:4, from pairToPair.cpp:12: /usr/include/c++/7/bits/stl_vector.h: In member function ‘bool PairToPair::FindHitsOnBothEnds(const BEDPE&, const std::vector&, const std::vector&)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h: In member function ‘void PairToPair::FindHitsOnEitherEnd(const BEDPE&, const std::vector&, const std::vector&)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/reldist make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling randomBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/sampleFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling sampleHelp.cpp * compiling pairToBed.cpp 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; ^~~~~~~~~~ In file included from /usr/include/c++/7/vector:69:0, from ../utils//lineFileUtilities/lineFileUtilities.h:4, from pairToBed.cpp:12: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from ../utils//lineFileUtilities/lineFileUtilities.h:4, from pairToBed.cpp:12: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void BedIntersectPE::FindOverlaps(const BEDPE&, std::vector&, std::vector&, const string&)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/shiftBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling reldistMain.cpp compiling RegressTest.cpp 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 make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/shuffleBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling sampleFile.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/slopBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling shiftBedMain.cpp * compiling reldist.cpp reldist.cpp: In member function ‘void RelativeDistance::ReportDistanceSummary()’: reldist.cpp:73:62: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘unsigned int’ [-Wformat=] reldist.cpp:71:16: freqItr->second, ~~~~~~~~~~~~~~~ reldist.cpp:73:62: (float) freqItr->second / (float) _tot_queries); ^ reldist.cpp:73:62: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/sortBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling slopBedMain.cpp * compiling shuffleBedMain.cpp * compiling shiftBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/spacingFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling sortMain.cpp * compiling spacingHelp.cpp * compiling slopBed.cpp slopBed.cpp: In member function ‘void BedSlop::AddSlop(BED&)’: slopBed.cpp:81:53: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (((int)bed.start - (long)_rightSlop) >= chromSize && _rightSlop < 0) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ slopBed.cpp:91:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( ((int)bed.end + (long)_leftSlop) <= chromSize ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ slopBed.cpp:108:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if( ((int)bed.start - (long)_leftSlop) >= chromSize && _leftSlop < 0) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ slopBed.cpp:120:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( ((int)bed.end + (long)_rightSlop) <= chromSize ) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/split make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling spacingFile.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/subtractFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling subtractHelp.cpp * compiling shuffleBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/tagBam make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling subtractFile.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/unionBedGraphs make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling tagBamMain.cpp * compiling sortBed.cpp In file included from /usr/include/c++/7/vector:69:0, from ../utils//lineFileUtilities/lineFileUtilities.h:4, from sortBed.cpp:13: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from ../utils//bedFile/bedFile.h:29, from sortBed.h:12, from sortBed.cpp:14: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_algo.h:1880:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __final_insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1880:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from ../utils//bedFile/bedFile.h:29, from sortBed.h:12, from sortBed.cpp:14: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = BED; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~~~ /usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~~ /usr/include/c++/7/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/algorithm:62:0, from ../utils//bedFile/bedFile.h:29, from sortBed.h:12, from sortBed.cpp:14: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from ../utils//bedFile/bedFile.h:29, from sortBed.h:12, from sortBed.cpp:14: /usr/include/c++/7/bits/stl_heap.h:408:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__pop_heap(__first, __last, __last, __comp); ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from ../utils//bedFile/bedFile.h:29, from sortBed.h:12, from sortBed.cpp:14: /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1672:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__make_heap(__first, __middle, __comp); ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from ../utils//lineFileUtilities/lineFileUtilities.h:4, from sortBed.cpp:13: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void BedSort::SortBedBySizeDesc()’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from ../utils//bedFile/bedFile.h:29, from sortBed.h:12, from sortBed.cpp:14: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1971:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In member function ‘void BedSort::SortBedByChromThenSizeDesc()’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1971:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In member function ‘void BedSort::SortBedByChromThenSizeAsc()’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1971:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In member function ‘void BedSort::SortBedByChromThenScoreDesc()’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1971:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In member function ‘void BedSort::SortBedByChromThenScoreAsc()’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1971:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from ../utils//lineFileUtilities/lineFileUtilities.h:4, from sortBed.cpp:13: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void BedSort::SortBedBySizeAsc()’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from ../utils//bedFile/bedFile.h:29, from sortBed.h:12, from sortBed.cpp:14: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1971:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/windowBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling unionBedGraphsMain.cpp 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 splitBed.cpp In file included from /usr/include/c++/7/vector:69:0, from ../utils//lineFileUtilities/lineFileUtilities.h:4, from splitBed.cpp:16: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BED&}; _Tp = BED; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from ../utils//lineFileUtilities/lineFileUtilities.h:4, from splitBed.cpp:16: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void BedSplit::loadBed()’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from ../utils//bedFile/bedFile.h:29, from splitBed.h:10, from splitBed.cpp:18: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from ../utils//bedFile/bedFile.h:29, from splitBed.h:10, from splitBed.cpp:18: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = BED; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~~~ /usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~~ /usr/include/c++/7/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/algorithm:62:0, from ../utils//bedFile/bedFile.h:29, from splitBed.h:10, from splitBed.cpp:18: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from ../utils//bedFile/bedFile.h:29, from splitBed.h:10, from splitBed.cpp:18: /usr/include/c++/7/bits/stl_heap.h:408:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__pop_heap(__first, __last, __last, __comp); ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from ../utils//bedFile/bedFile.h:29, from splitBed.h:10, from splitBed.cpp:18: /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1672:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__make_heap(__first, __middle, __comp); ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In member function ‘int BedSplit::doEuristicSplitOnTotalSize()’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ * compiling splitBedMain.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/windowMaker make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * compiling tagBam.cpp * compiling windowMain.cpp * compiling unionBedGraphs.cpp * compiling windowMaker.cpp * compiling windowMakerMain.cpp * compiling windowBed.cpp make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building main bedtools binary. done. - Creating executables for old CLI. done. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' dh_auto_test -a make -j4 -O test make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' $CXXFLAGS is [-Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Isrc/utils/bedFile -Isrc/utils/BinTree -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep -Isrc/utils/Contexts -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders -Isrc/utils/FileRecordTools/Records -Isrc/utils/general -Isrc/utils/gzstream -Isrc/utils/fileType -Isrc/utils/gzstream/ -Isrc/utils/lineFileUtilities -Isrc/utils/KeyListOps -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile -Isrc/utils/BamTools -Isrc/utils/BamTools/include -Isrc/utils/BamTools/src -Isrc/utils/BamTools-Ancillary -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: ========================================================= make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' DETECTED_VERSION = v2.27.1 CURRENT_VERSION = v2.27.1 make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' * Creating BamTools API make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/FileRecordTools make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/FileRecordTools/FileReaders make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/FileRecordTools/Records make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/bedFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BinTree make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//bedFile.o' is up to date. make[2]: Nothing to be done for 'all'. - Building in FileReaders - Building in Records make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/version make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[3]: Nothing to be done for 'all'. make[2]: '../../../obj//BinTree.o' is up to date. make[3]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/chromsweep make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/bedGraphFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. - Building in src/utils/Contexts make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//bedGraphFile.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/general make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//chromsweep.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/gzstream make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/fileType make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//gzstream.o' is up to date. 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[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/bedFilePE make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/KeyListOps make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/NewChromsweep make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/sequenceUtilities make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//bedFilePE.o' is up to date. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/tabFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BamTools make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BamTools-Ancillary make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//sequenceUtils.o' is up to date. make[2]: '../../../obj//tabFile.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/BlockedIntervals make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/Fasta make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/VectorOps make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/GenomeFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/RecordOutputMgr make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//NewGenomeFile.o' is up to date. make[2]: '../../../obj//VectorOps.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/ToolBase make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/utils/driver make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: '../../../obj//RecordOutputMgr.o' is up to date. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/annotateBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bamToBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: '../../../obj//ToolBase.o' is up to date. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bedToBam make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bamToFastq make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bedpeToBam make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' 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[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bedToIgv make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/bed12ToBed6 make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/closestFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/clusterBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' 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[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/complementFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/expand make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/fastaFromBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/coverageFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/flankBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/genomeCoverageBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/getOverlap make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/groupBy make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/intersectFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/fisher make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/jaccard make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/linksBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' 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[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/maskFastaFromBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/mapFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/mergeFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/multiBamCov make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/multiIntersectBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/nucBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/pairToBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' 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[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/pairToPair make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/randomBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/regressTest make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/reldist make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/sampleFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/shiftBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' 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[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/slopBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/shuffleBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/sortBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' 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[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/spacingFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/split make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/subtractFile make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/tagBam make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/unionBedGraphs make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/windowBed make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building in src/windowMaker make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. make[2]: Nothing to be done for 'all'. compiling RegressTest.cpp 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 make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' - Building main bedtools binary. done. - Creating executables for old CLI. done. make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' make[1]: Entering directory '/<>/bedtools-2.27.1+dfsg' Testing bedtools bamtobed: bamtobed.t1...ok bamtobed.t2...ok bamtobed.t3...ok bamtobed.t4...ok bamtobed.t5...ok bamtobed.t6...ok bamtobed.t7...ok bamtobed.t8...ok bamtobed.t9...ok bamtobed.t10...ok bamtobed.t9...ok bamtobed.t11...ok Testing bedtools bamtofastq: ok ok Testing bedtools bed12tobed6: bed12tobed6.t1...ok bed12tobed6.t2...ok bed12tobed6.t3...ok bed12tobed6.t4...ok bed12tobed6.t5...ok Testing bedtools closest: closest.t1...ok closest.t2...ok closest.t3...ok closest.t4...ok closest.t5...ok closest.t6...ok closest.t7...ok closest.t8...ok closest.t9...ok closest.t10...ok closest.t11...ok closest.t13...ok closest.t14...ok closest.t15...ok closest.t16...ok closest.t17...ok closest.t18...ok closest.t19...ok closest.t20...ok closest.t21...ok closest.t22...ok closest.t23...ok closest.t24...ok closest.t25...ok closest.t26...ok closest.t27...ok closest.t28...ok closest.t29...ok closest.t30...ok closest.t31...ok closest.t32...ok closest.t33...ok closest.t34...ok closest.t35...ok closest.t36...ok closest.t37...ok closest.t38...ok closest.t39...ok closest.t40...ok closest.t41...ok closest.t42...ok closest.t43...ok closest.t44...ok closest.t45...ok closest.t46...ok closest.t47...ok closest.t48...ok closest.t49...ok closest.t50...ok closest.t51...ok closest.t52...ok closest.t53...ok closest.t54...ok closest.t55...ok closest.t56...ok closest.t57...ok closest.t58...ok closest.t59...ok closest.t60...ok closest.t61...ok closest.t62...ok closest.t63...ok closest.t64...ok closest.t65...ok closest.t66...ok closest.t67...ok closest.t68...ok closest.t69...ok closest.t70...ok closest.t71...ok ########################################################### # # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS # ########################################################### closest.t01...ok closest.t02...ok closest.t03...ok closest.t04...ok closest.t05...ok closest.t06...ok closest.t07...ok closest.t08...ok closest.t09...ok closest.t10...ok closest.t11...ok closest.t12...ok closest.t13...ok closest.t14...ok closest.t15...ok closest.t16...ok closest.t17...ok closest.t18...ok closest.t19...ok closest.20...ok closest.21...ok closest.22...ok closest.23...ok ########################################################### # # K CLOSEST HITS TESTS # ########################################################### kclosest.t1...ok kclosest.t2...ok kclosest.t3...ok kclosest.t4...ok kclosest.t5...ok kclosest.t6...ok kclosest.t7...ok kclosest.t8...ok kclosest.t9...ok kclosest.t10...ok kclosest.t11...ok kclosest.t12...ok kclosest.t13...ok kclosest.t14...ok kclosest.t15...ok kclosest.t16...ok kclosest.t17...ok kclosest.t18...ok kclosest.t19...ok kclosest.t20...ok kclosest.t21...ok kclosest.t22...ok kclosest.t23...ok kclosest.t24...ok kclosest.t25...ok kclosest.t26...ok kclosest.t27...ok kclosest.t28...ok kclosest.t29...ok kclosest.t30...ok kclosest.t31...ok kclosest.t32...ok kclosest.t33...ok kclosest.t34...ok kclosest.t35...ok kclosest.t36...ok kclosest.t37...ok kclosest.t38...ok kclosest.t39...ok kclosest.t40...ok kclosest.t41...ok kclosest.t42...ok kclosest.t43...ok kclosest.t44...ok kclosest.t45...ok Testing bedtools cluster: cluster.t1...ok cluster.t2...ok Testing bedtools complement: complement.t1...ok complement.t2...ok complement.t3...ok complement.t4...ok complement.t5...ok complement.t6...ok complement.t7...ok complement.t8...ok complement.t9...ok Testing bedtools coverage: coverage.t1...ok coverage.t1b...ok coverage.t2...ok coverage.t2b...ok coverage.t3...ok coverage.t3b...ok coverage.t4...ok coverage.t4b...ok coverage.t5...ok coverage.t5b...ok coverage.t6...ok coverage.t6b...ok coverage.t7...ok coverage.t7b...ok coverage.t8...ok coverage.t8b...ok coverage.t9...ok coverage.t9b...ok coverage.t10...ok coverage.t10b...ok coverage.t11...ok coverage.t11b...ok coverage.t12...ok coverage.t12b...ok coverage.t13...ok coverage.t13b...ok coverage.t14...ok coverage.t14b...ok coverage.t15...ok coverage.t15b...ok coverage.t16...ok coverage.t16b...ok coverage.t17...ok coverage.t17b...ok coverage.t18...ok coverage.t18b...ok coverage.t19...ok coverage.t19b...ok coverage.t20...ok Testing bedtools expand: expand.t1...ok expand.t2...ok expand.t3...ok Testing bedtools fisher: fisher.t1...ok fisher.t2...ok fisher.t3...ok fisher.t4...ok Testing bedtools flank: flank.t1...ok flank.t2...ok flank.t3...ok flank.t4...ok flank.t5...ok flank.t6...ok flank.t7...ok flank.t8...ok flank.t9...ok flank.t10...ok flank.t11...ok Testing bedtools general: general.t01...ok general.t02...ok general.t03...ok general.t05...ok general.t06...ok general.t07...ok general.t08...ok general.t09...ok general.t10...ok general.t11...ok general.t12...ok general.t13...ok general.t14...ok general.15...ok general.t16...ok general.t17...ok general.t18...ok general.t19...ok general.t20...ok general.t21...ok general.22...ok general.t23...ok general.t24...ok general.t25...ok general.t26...ok general.t27...ok general.t28...ok general.29...ok general.t30...ok general.t31...ok general.t32...ok general.t33...ok general.t34...ok general.t35...ok general.36...ok general.t37...ok general.t38...ok general.t39...ok general.t40...ok general.t41...ok general.t42...ok general.t43...ok general.t44...ok general.t45...ok general.t46...ok Testing bedtools genomecov: genomecov.t1...ok genomecov.t2...ok genomecov.t3...ok genomecov.t4...ok genomecov.t5...ok genomecov.t6...ok genomecov.t7...ok genomecov.t8...ok genomecov.t9...ok genomecov.t10...ok genomecov.t11...ok genomecov.t12...ok genomecov.t13...ok genomecov.t14...ok genomecov.t15...ok Testing bedtools getfasta: getfasta.t01...ok getfasta.t02...ok getfasta.t03...ok getfasta.t04...ok getfasta.t05...ok getfasta.t06...ok getfasta.t07...ok getfasta.t08...index file test.iupac.fa.fai not found, generating... ok getfasta.t09...index file test.iupac.fa.fai not found, generating... ok getfasta.t10...index file test.fa.fai not found, generating... ok getfasta.t11...ok getfasta.t12...ok getfasta.t13...ok getfasta.t14...ok getfasta.t15...ok getfasta.t134..ok Testing bedtools groupby: groupby.t1...ok groupby.t2...ok groupby.t3...ok groupby.t4...ok groupby.t5...ok groupby.t6...ok groupby.t7...ok groupby.t8...ok groupby.t9...ok groupby.t10...ok groupby.t11...ok groupby.t12...ok groupby.t13...ok groupby.t14...ok groupby.t16...ok groupby.t17...ok groupby.t18...ok groupby.t19...\c ok groupby.t20...\c ok Testing bedtools intersect: intersect.t01...ok intersect.t02...ok intersect.t03...ok intersect.t04...ok intersect.t05...ok intersect.t06...ok intersect.t07...ok intersect.t08...ok intersect.t09...ok intersect.t10...ok intersect.t11...ok intersect.t12...ok intersect.t13...ok intersect.t14...ok intersect.t15...ok intersect.t16...ok intersect.t17...ok intersect.t18...ok intersect.t19...ok intersect.t20...ok intersect.t21...ok intersect.t22...ok intersect.t22.a...ok intersect.t22.b...ok intersect.t22.c...ok intersect.t22.d...ok intersect.t22.e...ok intersect.t22.f...ok intersect.t22.g...ok intersect.t23...ok intersect.t24...ok intersect.t25...ok intersect.t26...ok intersect.t27...ok intersect.t28...ok intersect.t29...ok intersect.t30...ok intersect.t31...ok intersect.t32...ok intersect.t33...ok intersect.t34...ok intersect.t35...ok intersect.t36...ok intersect.t37...ok intersect.t38...ok intersect.t39...ok intersect.t40...ok intersect.t41...ok intersect.t42...ok intersect.t43...ok intersect.t44...ok intersect.t45...ok intersect.t46...ok intersect.t47...ok intersect.t48...ok intersect.t49...ok intersect.t50...ok intersect.t51...ok intersect.t52...ok intersect.t53...ok intersect.t54...ok intersect.t55...ok intersect.t56...ok intersect.t57...ok intersect.t58...ok intersect.t59...ok intersect.t60...ok intersect.t61...ok intersect.t62...ok intersect.t63...ok intersect.t64...ok intersect.t65...ok intersect.t66...ok intersect.t67...ok intersect.t68...ok intersect.t69...ok intersect.t70...ok intersect.t71...ok intersect.t72...ok intersect.t73...ok intersect.t74...ok intersect.t75...ok intersect.t76...ok intersect.t77...ok intersect.t78...ok intersect.t79...ok intersect.t80...ok intersect.t81...ok intersect.t82...ok intersect.new.t01...ok intersect.new.t02...ok intersect.new.t03...ok intersect.new.t04...ok intersect.new.t05...ok intersect.new.t06...ok intersect.new.t07...ok intersect.new.t08...ok intersect.new.t09...ok intersect.new.t10...ok intersect.new.t11...ok intersect.new.t12...ok intersect.new.t13...ok intersect.new.t14...ok intersect.new.t15...ok intersect.new.t16...ok intersect.new.t17...ok intersect.new.t18...ok intersect.new.t19...ok intersect.new.t20...ok intersect.new.t20.b...ok intersect.new.t20.c...ok intersect.new.t21...ok intersect.new.t22...ok intersect.new.t23...ok intersect.new.t24...ok intersect.new.t25...ok intersect.new.t26...ok intersect.new.t27...ok intersect.new.t28...ok intersect.new.t29...ok intersect.new.t30...ok intersect.new.t31...ok intersect.new.t32...ok intersect.new.t33...ok intersect.new.t34...ok intersect.new.t35...ok intersect.new.t36...ok intersect.new.t37...ok intersect.new.t38...ok intersect.new.t39...ok intersect.new.t40...ok intersect.new.t41...ok intersect.new.t42...ok intersect.new.t43...ok intersect.new.t44...ok intersect.new.t45...ok intersect.new.t46...ok intersect.new.t47...ok intersect.new.t48...ok intersect.new.t49...ok intersect.new.t50...ok intersect.new.t51...ok intersect.new.t52...ok intersect.new.t53...ok intersect.new.t54...ok intersect.new.t55...ok intersect.new.t56...ok intersect.new.t57...ok intersect.new.t58...ok intersect.new.t59...ok intersect.new.t60...ok intersect.new.t61...ok intersect.new.t62...ok intersect.new.t63...ok intersect.new.t64...ok intersect.new.t65...ok intersect.new.t66...ok intersect.new.t67a...ok intersect.new.t67b...ok intersect.new.t68a...ok intersect.new.t68b...ok intersect.new.t69...ok intersect.new.t70...ok intersect.new.t71...ok intersect.new.t72...ok ########################################################### # # MULTIPLE DATABASE INTERSECTION # ########################################################### intersect.t01...ok intersect.t02...ok intersect.t03...ok intersect.t04...ok intersect.t05...ok intersect.t06...ok intersect.t07...ok intersect.t08...ok intersect.t09...ok intersect.t10...ok intersect.t11...ok intersect.t12...ok intersect.t13...ok intersect.t13...ok intersect.t14...ok intersect.t15...ok intersect.t16...ok intersect.t17...ok intersect.t18...ok intersect.t19...ok ########################################################### # # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS # ########################################################### intersect.t01...ok intersect.t02...ok intersect.t03...ok intersect.t04...ok intersect.t05...ok intersect.t06...ok intersect.t07...ok intersect.t08...ok intersect.t09...ok intersect.t10...ok intersect.t11...ok intersect.t12...ok intersect.t13...ok intersect.t14...ok intersect.t15...ok intersect.t16...ok intersect.t17...ok intersect.t18...ok intersect.t19...ok intersect.20...ok intersect.21...ok intersect.22...ok intersect.23...ok Testing bedtools jaccard: jaccard.t01...ok jaccard.t02...ok jaccard.t03...ok jaccard.t05...ok jaccard.t06...ok jaccard.t07...ok jaccard.t08...ok jaccard.t09...ok jaccard.t10...ok jaccard.t11...ok jaccard.t12...ok jaccard.t13...ok Testing bedtools makewindows: makewindows.t01...ok makewindows.t02...ok makewindows.t03...ok makewindows.t04...ok makewindows.t05...ok makewindows.t06...ok makewindows.t07...ok makewindows.t08...ok makewindows.t09...ok Testing bedtools map: map.t01...ok map.t02...ok map.t03...ok map.t04...ok map.t05...ok map.t06...ok map.t07...ok map.t08...ok map.t09...ok map.t10...ok map.t11...ok map.t12...ok map.t13...ok map.t14...ok map.t15...ok map.t16...ok map.t17...ok map.t18...ok map.t19...ok map.t20...ok map.t21...ok map.t22..ok map.t23..ok map.t24..ok map.t25..ok map.t26..ok map.t27..ok map.t28..ok map.t29..ok map.t30..ok map.t31..ok map.t32..ok map.t33..ok map.t33..ok map.t33..ok map.t34..ok map.t35..ok map.t36..ok map.t37..ok map.t38..ok map.t39..ok map.t40..ok map.t41..ok map.t42..ok map.t43..ok map.t44...ok map.t45...ok map.t46...ok map.t47...ok map.t48...ok map.t49...ok map.t50...ok map.t51...ok map.t52...ok map.t53...ok map.t54...ok map.t55...ok Testing bedtools merge: merge.t1...ok merge.t2...ok merge.t3...ok merge.t4...ok merge.t5...ok merge.t6...ok merge.t7...ok merge.t8...ok merge.t9a...ok merge.t9b...ok merge.t10...ok merge.t11...ok merge.t12...ok merge.t13...ok merge.t14...ok merge.t15...ok merge.t16...ok merge.t17...ok merge.t18...ok merge.t19...ok merge.t20...ok merge.t21...ok merge.t22...ok merge.t23a...ok merge.t23b...ok merge.t24...ok merge.t25...ok merge.t26...ok merge.t27...ok merge.t28...ok merge.t29...ok merge.t30...ok merge.t31...ok merge.t32...ok merge.t33...ok merge.t34...ok merge.t35...ok merge.t36...ok merge.t37...ok merge.t38...ok merge.t39...ok merge.t40...ok merge.t41...ok merge.t42...ok merge.t43...ok merge.t44a...ok merge.t44b...skipped - could not find vcfSVtest.2.vcf merge.t45...ok merge.t46...ok merge.t47...ok merge.t48...ok merge.t49...ok Testing bedtools multicov: multicov.t1...ok multicov.t2...ok multicov.t3...ok multicov.t4...ok multicov.t5...ok multicov.t6...ok multicov.t7...ok multicov.t8...ok multicov.t9...ok Testing bedtools negativecontrol: Testing bedtools reldist: reldist.t01...ok reldist.t02...ok reldist.t03...ok Testing bedtools sample: sample.t01...ok sample.new.t02...ok sample.new.t03...ok sample.new.t04...ok sample.new.t05...ok sample.new.t06...ok sample.new.t07...ok sample.new.t08...ok sample.new.t09...ok Testing bedtools shift: shift.t1...ok shift.t2...ok shift.t3...ok shift.t3...ok shift.t4...ok shift.t5...ok shift.t6...ok shift.t7...ok shift.t8...ok shift.t9...ok shift.t10...ok Testing bedtools shuffle: shuffle.t1...1,10c1,10 < chr2 34697611 34698079 trf 789 < chr4 97373990 97374163 trf 346 < chr1 211569500 211569740 trf 434 < chr15 100895645 100895867 trf 273 < chr10 79193410 79193587 trf 187 < chr2 180138393 180138558 trf 199 < chr11 1280504 1280642 trf 242 < chr2 194322764 194322799 trf 70 < chr18 24454309 24454406 trf 79 < chr18 58907072 58907113 trf 73 --- > chr1 49390118 49390586 trf 789 > chr13 60419956 60420129 trf 346 > chr9 88507701 88507941 trf 434 > chr1 176220424 176220646 trf 273 > chr7 69225121 69225298 trf 187 > chr2 25938602 25938767 trf 199 > chr7 133111177 133111315 trf 242 > chr3 5894626 5894661 trf 70 > chr7 144738233 144738330 trf 79 > chr9 28526037 28526078 trf 73 fail shuffle.t2...1c1 < chr1 2158771 2159239 trf 789 --- > chr1 3126067 3126535 trf 789 3,20c3,20 < chr1 1837113 1837353 trf 434 < chr1 1389014 1389236 trf 273 < chr1 458954 459131 trf 187 < chr4 267572 267737 trf 199 < chr2 608295 608433 trf 242 < chr1 285876 285911 trf 70 < chr1 1344769 1344866 trf 79 < chr1 548923 548964 trf 73 < chr1 95584 95616 trf 64 < chr1 1063033 1063138 trf 149 < chr1 4349564 4349602 trf 58 < chr1 3052376 3052846 trf 278 < chr1 1922714 1923184 trf 339 < chr2 389822 390250 trf 202 < chr1 1427519 1427562 trf 59 < chr1 1280827 1280867 trf 62 < chr1 3745294 3745329 trf 52 < chr1 4151677 4151854 trf 302 --- > chr3 747335 747575 trf 434 > chr2 451924 452146 trf 273 > chr1 1837113 1837290 trf 187 > chr1 1389014 1389179 trf 199 > chr1 458954 459092 trf 242 > chr4 267572 267607 trf 70 > chr2 608295 608392 trf 79 > chr3 544706 544747 trf 73 > chr1 285876 285908 trf 64 > chr5 961111 961216 trf 149 > chr4 53213 53251 trf 58 > chr1 1344769 1345239 trf 278 > chr1 1516219 1516689 trf 339 > chr1 1062880 1063308 trf 202 > chr1 2030329 2030372 trf 59 > chr1 4349564 4349604 trf 62 > chr1 3052376 3052411 trf 52 > chr1 2890010 2890187 trf 302 fail shuffle.t3...1c1 < chr1 2158771 2159239 trf 789 --- > chr1 3126067 3126535 trf 789 3,20c3,20 < chr1 1837113 1837353 trf 434 < chr1 1389014 1389236 trf 273 < chr1 458954 459131 trf 187 < chr4 267572 267737 trf 199 < chr2 608295 608433 trf 242 < chr1 285876 285911 trf 70 < chr1 1344769 1344866 trf 79 < chr1 548923 548964 trf 73 < chr1 95584 95616 trf 64 < chr1 1063033 1063138 trf 149 < chr1 4349564 4349602 trf 58 < chr1 3052376 3052846 trf 278 < chr1 1922714 1923184 trf 339 < chr2 389822 390250 trf 202 < chr1 1427519 1427562 trf 59 < chr1 1280827 1280867 trf 62 < chr1 3745294 3745329 trf 52 < chr1 4151677 4151854 trf 302 --- > chr3 747335 747575 trf 434 > chr2 451924 452146 trf 273 > chr1 1837113 1837290 trf 187 > chr1 1389014 1389179 trf 199 > chr1 458954 459092 trf 242 > chr4 267572 267607 trf 70 > chr2 608295 608392 trf 79 > chr3 544706 544747 trf 73 > chr1 285876 285908 trf 64 > chr5 961111 961216 trf 149 > chr4 53213 53251 trf 58 > chr1 1344769 1345239 trf 278 > chr1 1516219 1516689 trf 339 > chr1 1062880 1063308 trf 202 > chr1 2030329 2030372 trf 59 > chr1 4349564 4349604 trf 62 > chr1 3052376 3052411 trf 52 > chr1 2890010 2890187 trf 302 fail shuffle.t4...ok shuffle.t5...1,10c1,10 < chr2 34697611 34698079 trf 789 < chr4 97373990 97374163 trf 346 < chr1 211569500 211569740 trf 434 < chr1 211569500 211569740 trf 434 < chr5 12248678 12248716 trf 58 < chr1 10051107 10051141 trf 68 < chr3 63788079 63788115 trf 63 < chr1 56972561 56972612 trf 66 < chr1 56972561 56972612 trf 66 < chr5 27921185 27921353 trf 150 --- > chr1 49390118 49390586 trf 789 > chr1 49390118 49390586 trf 789 > chr1 176220424 176220646 trf 273 > chr1 176220424 176220646 trf 273 > chr2 25938602 25938767 trf 199 > chr3 5894626 5894661 trf 70 > chr2 57803306 57803344 trf 58 > chr4 13407024 13407058 trf 68 > chr3 18198257 18198308 trf 66 > chr1 71587801 71587968 trf 159 fail shuffle.t6...ok Testing bedtools slop: slop.t1...ok slop.t2...ok slop.t3...ok slop.t4...ok slop.t5...ok slop.t6...ok slop.t7...ok slop.t8...ok slop.t9...ok slop.t10...ok slop.t11...ok slop.t12...ok slop.t13...ok slop.t14...ok slop.t15...ok slop.t16...ok slop.t17...ok slop.t18...ok slop.t19...ok slop.t20...ok slop.t21...ok slop.t22...ok Testing bedtools sort: sort.t01...ok sort.t02...ok sort.t03...ok sort.t04...ok sort.t05...ok sort.t06...ok sort.t07...ok sort.t08...ok sort.t09...ok sort.t10...ok Testing bedtools spacing: spacing.t01...ok Testing bedtools split: split.01.size...ok split.02.simple...ok spliit.03.simple...ok Testing bedtools subtract: subtract.t1...ok subtract.t2...ok subtract.t3...ok subtract.t4...ok subtract.t5...ok subtract.t6...ok subtract.t7...ok subtract.t8...ok subtract.t9...ok subtract.t10...ok subtract.t11...ok subtract.t12...ok subtract.t13...ok subtract.t14...ok subtract.t15...ok subtract.t16...ok subtract.t17...ok subtract.t18...ok subtract.t19...ok subtract.t20...ok subtract.t21...ok -------------------------- Test Results -------------------------- Tools passing: bamtobed bamtofastq bed12tobed6 closest cluster complement coverage expand fisher flank general genomecov getfasta groupby intersect jaccard makewindows map merge multicov reldist sample shift slop sort spacing split subtract Tools failing: negativecontrol shuffle NB: the 'negativecontrol' test is supposed to fail. If it wasn't caught, something went wrong with this test script. Makefile:196: recipe for target 'test' failed make[1]: *** [test] Error 1 make[1]: Leaving directory '/<>/bedtools-2.27.1+dfsg' dh_auto_test: make -j4 -O test returned exit code 2 debian/rules:10: recipe for target 'build-arch' failed make: *** [build-arch] Error 25 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20180421-1229 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 61688 Build-Time: 171 Distribution: bionic-proposed Fail-Stage: build Host Architecture: armhf Install-Time: 21 Job: bedtools_2.27.1+dfsg-1.dsc Machine Architecture: arm64 Package: bedtools Package-Time: 197 Source-Version: 2.27.1+dfsg-1 Space: 61688 Status: attempted Version: 2.27.1+dfsg-1 -------------------------------------------------------------------------------- Finished at 20180421-1229 Build needed 00:03:17, 61688k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14333850 Scanning for processes to kill in build PACKAGEBUILD-14333850 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14333850 Stopping target for build PACKAGEBUILD-14333850 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14333850 Removing build PACKAGEBUILD-14333850