https://launchpad.net/ubuntu/+archive/test-rebuild-20221116-xenial-release/+build/24758162 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-035 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 aarch64 Buildd toolchain package versions: launchpad-buildd_223~593~ubuntu20.04.1 python3-lpbuildd_223~593~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.6 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 3 Dec 11:09:06 ntpdate[1870]: adjust time server 10.211.37.1 offset 0.006753 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=xenial --arch=armhf PACKAGEBUILD-24758162 --image-type chroot /home/buildd/filecache-default/181062a90b26646e87edd030d787a50801aeed8c Creating target for build PACKAGEBUILD-24758162 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=xenial --arch=armhf PACKAGEBUILD-24758162 Starting target for build PACKAGEBUILD-24758162 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=xenial --arch=armhf PACKAGEBUILD-24758162 'deb http://ftpmaster.internal/ubuntu xenial main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-24758162 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=xenial --arch=armhf PACKAGEBUILD-24758162 Updating target for build PACKAGEBUILD-24758162 Hit:1 http://ftpmaster.internal/ubuntu xenial InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24758162 armhf xenial -c chroot:build-PACKAGEBUILD-24758162 --arch=armhf --dist=xenial --nolog bamtools_2.4.0+dfsg-3build1.dsc Initiating build PACKAGEBUILD-24758162 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 armv7l sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-035.buildd +==============================================================================+ | bamtools 2.4.0+dfsg-3build1 (armhf) Sat, 03 Dec 2022 11:09:20 +0000 | +==============================================================================+ Package: bamtools Version: 2.4.0+dfsg-3build1 Source Version: 2.4.0+dfsg-3build1 Distribution: xenial Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24758162/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/bamtools-EfhdJX/resolver-DE7oiw' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bamtools_2.4.0+dfsg-3build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/bamtools-EfhdJX/bamtools-2.4.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/bamtools-EfhdJX' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 9.0.0), d-shlibs (>= 0.56), cmake, zlib1g-dev, libjsoncpp-dev, help2man, doxygen, build-essential, fakeroot Filtered Build-Depends: debhelper (>= 9.0.0), d-shlibs (>= 0.56), cmake, zlib1g-dev, libjsoncpp-dev, help2man, doxygen, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [413 B] Get:5 copy:/<>/apt_archive ./ Packages [494 B] Fetched 1864 B in 0s (80.8 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autotools-dev bsdmainutils cmake cmake-data d-shlibs debhelper dh-strip-nondeterminism doxygen file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libarchive13 libasprintf0v5 libbsd0 libclang1-3.6 libcroco3 libcurl3 libedit2 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libjsoncpp-dev libjsoncpp1 libllvm3.6v5 liblocale-gettext-perl liblzo2-2 libmagic1 libobjc-5-dev libobjc4 libpipeline1 libtimedate-perl libunistring0 libxml2 man-db po-debconf zlib1g-dev Suggested packages: wamerican | wordlist whois vacation codeblocks eclipse ninja-build dh-make doxygen-latex doxygen-doc doxygen-gui graphviz gettext-doc autopoint groff lrzip less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xdg-user-dirs xml-core libmail-sendmail-perl The following NEW packages will be installed: autotools-dev bsdmainutils cmake cmake-data d-shlibs debhelper dh-strip-nondeterminism doxygen file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libarchive13 libasprintf0v5 libbsd0 libclang1-3.6 libcroco3 libcurl3 libedit2 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libjsoncpp-dev libjsoncpp1 libllvm3.6v5 liblocale-gettext-perl liblzo2-2 libmagic1 libobjc-5-dev libobjc4 libpipeline1 libtimedate-perl libunistring0 libxml2 man-db po-debconf sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 32.8 MB of archives. After this operation, 114 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [834 B] Get:2 http://ftpmaster.internal/ubuntu xenial/main armhf liblocale-gettext-perl armhf 1.07-1build1 [16.6 kB] Get:3 http://ftpmaster.internal/ubuntu xenial/main armhf groff-base armhf 1.22.3-7 [1023 kB] Get:4 http://ftpmaster.internal/ubuntu xenial/main armhf bsdmainutils armhf 9.0.6ubuntu3 [169 kB] Get:5 http://ftpmaster.internal/ubuntu xenial/main armhf libpipeline1 armhf 1.4.1-2 [21.0 kB] Get:6 http://ftpmaster.internal/ubuntu xenial/main armhf man-db armhf 2.7.5-1 [836 kB] Get:7 http://ftpmaster.internal/ubuntu xenial/main armhf cmake-data all 3.5.1-1ubuntu1 [1121 kB] Get:8 http://ftpmaster.internal/ubuntu xenial/main armhf liblzo2-2 armhf 2.08-1.2 [44.2 kB] Get:9 http://ftpmaster.internal/ubuntu xenial/main armhf libicu55 armhf 55.1-7 [7420 kB] Get:10 http://ftpmaster.internal/ubuntu xenial/main armhf libxml2 armhf 2.9.3+dfsg1-1 [602 kB] Get:11 http://ftpmaster.internal/ubuntu xenial/main armhf libarchive13 armhf 3.1.2-11build1 [232 kB] Get:12 http://ftpmaster.internal/ubuntu xenial/main armhf libcurl3 armhf 7.47.0-1ubuntu2 [161 kB] Get:13 http://ftpmaster.internal/ubuntu xenial/main armhf libexpat1 armhf 2.1.0-7 [52.4 kB] Get:14 http://ftpmaster.internal/ubuntu xenial/main armhf libjsoncpp1 armhf 1.7.2-1 [65.4 kB] Get:15 http://ftpmaster.internal/ubuntu xenial/main armhf cmake armhf 3.5.1-1ubuntu1 [2307 kB] Get:16 http://ftpmaster.internal/ubuntu xenial/main armhf libunistring0 armhf 0.9.3-5.2ubuntu1 [250 kB] Get:17 http://ftpmaster.internal/ubuntu xenial/main armhf libmagic1 armhf 1:5.25-2ubuntu1 [211 kB] Get:18 http://ftpmaster.internal/ubuntu xenial/main armhf file armhf 1:5.25-2ubuntu1 [20.9 kB] Get:19 http://ftpmaster.internal/ubuntu xenial/main armhf libbsd0 armhf 0.8.2-1 [48.2 kB] Get:20 http://ftpmaster.internal/ubuntu xenial/main armhf libasprintf0v5 armhf 0.19.7-2ubuntu3 [6158 B] Get:21 http://ftpmaster.internal/ubuntu xenial/main armhf gettext-base armhf 0.19.7-2ubuntu3 [44.5 kB] Get:22 http://ftpmaster.internal/ubuntu xenial/main armhf libedit2 armhf 3.1-20150325-1ubuntu2 [62.2 kB] Get:23 http://ftpmaster.internal/ubuntu xenial/main armhf libglib2.0-0 armhf 2.48.0-1ubuntu4 [977 kB] Get:24 http://ftpmaster.internal/ubuntu xenial/main armhf autotools-dev all 20150820.1 [39.8 kB] Get:25 http://ftpmaster.internal/ubuntu xenial/universe armhf d-shlibs all 0.66ubuntu1 [9272 B] Get:26 http://ftpmaster.internal/ubuntu xenial/main armhf libcroco3 armhf 0.6.11-1 [70.0 kB] Get:27 http://ftpmaster.internal/ubuntu xenial/main armhf gettext armhf 0.19.7-2ubuntu3 [1013 kB] Get:28 http://ftpmaster.internal/ubuntu xenial/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:29 http://ftpmaster.internal/ubuntu xenial/main armhf po-debconf all 1.0.19 [234 kB] Get:30 http://ftpmaster.internal/ubuntu xenial/main armhf libarchive-zip-perl all 1.56-2 [84.1 kB] Get:31 http://ftpmaster.internal/ubuntu xenial/main armhf libfile-stripnondeterminism-perl all 0.015-1 [10.3 kB] Get:32 http://ftpmaster.internal/ubuntu xenial/main armhf libtimedate-perl all 2.3000-2 [37.5 kB] Get:33 http://ftpmaster.internal/ubuntu xenial/main armhf dh-strip-nondeterminism all 0.015-1 [4864 B] Get:34 http://ftpmaster.internal/ubuntu xenial/main armhf debhelper all 9.20160115ubuntu3 [739 kB] Get:35 http://ftpmaster.internal/ubuntu xenial/main armhf libllvm3.6v5 armhf 1:3.6.2-3ubuntu2 [7542 kB] Get:36 http://ftpmaster.internal/ubuntu xenial/main armhf libobjc4 armhf 5.3.1-14ubuntu2 [91.9 kB] Get:37 http://ftpmaster.internal/ubuntu xenial/main armhf libobjc-5-dev armhf 5.3.1-14ubuntu2 [345 kB] Get:38 http://ftpmaster.internal/ubuntu xenial/main armhf libclang1-3.6 armhf 1:3.6.2-3ubuntu2 [3255 kB] Get:39 http://ftpmaster.internal/ubuntu xenial/main armhf doxygen armhf 1.8.11-1 [3229 kB] Get:40 http://ftpmaster.internal/ubuntu xenial/universe armhf help2man armhf 1.47.3 [110 kB] Get:41 http://ftpmaster.internal/ubuntu xenial/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2ubuntu4 [161 kB] Get:42 http://ftpmaster.internal/ubuntu xenial/main armhf libjsoncpp-dev armhf 1.7.2-1 [77.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 32.8 MB in 2s (14.3 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 11893 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-1build1_armhf.deb ... Unpacking liblocale-gettext-perl (1.07-1build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.3-7_armhf.deb ... Unpacking groff-base (1.22.3-7) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6ubuntu3_armhf.deb ... Unpacking bsdmainutils (9.0.6ubuntu3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../libpipeline1_1.4.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.5-1_armhf.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../cmake-data_3.5.1-1ubuntu1_all.deb ... Unpacking cmake-data (3.5.1-1ubuntu1) ... 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Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../sbuild-build-depends-main-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up liblocale-gettext-perl (1.07-1build1) ... Setting up groff-base (1.22.3-7) ... Setting up bsdmainutils (9.0.6ubuntu3) ... 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 libpipeline1:armhf (1.4.1-2) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up cmake-data (3.5.1-1ubuntu1) ... Setting up liblzo2-2:armhf (2.08-1.2) ... Setting up libicu55:armhf (55.1-7) ... Setting up libxml2:armhf (2.9.3+dfsg1-1) ... Setting up libarchive13:armhf (3.1.2-11build1) ... Setting up libcurl3:armhf (7.47.0-1ubuntu2) ... Setting up libexpat1:armhf (2.1.0-7) ... Setting up libjsoncpp1:armhf (1.7.2-1) ... Setting up cmake (3.5.1-1ubuntu1) ... Setting up libunistring0:armhf (0.9.3-5.2ubuntu1) ... Setting up libmagic1:armhf (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up libbsd0:armhf (0.8.2-1) ... Setting up libasprintf0v5:armhf (0.19.7-2ubuntu3) ... Setting up gettext-base (0.19.7-2ubuntu3) ... Setting up libedit2:armhf (3.1-20150325-1ubuntu2) ... Setting up libglib2.0-0:armhf (2.48.0-1ubuntu4) ... No schema files found: doing nothing. Setting up autotools-dev (20150820.1) ... Setting up d-shlibs (0.66ubuntu1) ... Setting up libcroco3:armhf (0.6.11-1) ... Setting up gettext (0.19.7-2ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.19) ... Setting up libarchive-zip-perl (1.56-2) ... Setting up libfile-stripnondeterminism-perl (0.015-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libllvm3.6v5:armhf (1:3.6.2-3ubuntu2) ... Setting up libobjc4:armhf (5.3.1-14ubuntu2) ... Setting up libobjc-5-dev:armhf (5.3.1-14ubuntu2) ... Setting up libclang1-3.6:armhf (1:3.6.2-3ubuntu2) ... Setting up doxygen (1.8.11-1) ... Setting up help2man (1.47.3) ... Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2ubuntu4) ... Setting up libjsoncpp-dev:armhf (1.7.2-1) ... Setting up debhelper (9.20160115ubuntu3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.015-1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 arm64 (armv7l) Toolchain package versions: binutils_2.26-8ubuntu2 dpkg-dev_1.18.4ubuntu1 g++-5_5.3.1-14ubuntu2 gcc-5_5.3.1-14ubuntu2 libc6-dev_2.23-0ubuntu3 libstdc++-5-dev_5.3.1-14ubuntu2 libstdc++6_5.3.1-14ubuntu2 linux-libc-dev_4.4.0-21.37 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.2.10ubuntu1 apt-transport-https_1.2.10ubuntu1 autotools-dev_20150820.1 base-files_9.4ubuntu4 base-passwd_3.5.39 bash_4.3-14ubuntu1 binutils_2.26-8ubuntu2 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.27.1-6ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8 ca-certificates_20160104ubuntu1 cmake_3.5.1-1ubuntu1 cmake-data_3.5.1-1ubuntu1 coreutils_8.25-2ubuntu2 cpp_4:5.3.1-1ubuntu1 cpp-5_5.3.1-14ubuntu2 d-shlibs_0.66ubuntu1 dash_0.5.8-2.1ubuntu2 debconf_1.5.58ubuntu1 debhelper_9.20160115ubuntu3 debianutils_4.7 dh-strip-nondeterminism_0.015-1 diffutils_1:3.3-3 doxygen_1.8.11-1 dpkg_1.18.4ubuntu1 dpkg-dev_1.18.4ubuntu1 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 file_1:5.25-2ubuntu1 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1ubuntu1 g++-5_5.3.1-14ubuntu2 gcc_4:5.3.1-1ubuntu1 gcc-5_5.3.1-14ubuntu2 gcc-5-base_5.3.1-14ubuntu2 gcc-6-base_6.0.1-0ubuntu1 gettext_0.19.7-2ubuntu3 gettext-base_0.19.7-2ubuntu3 gnupg_1.4.20-1ubuntu3 gpgv_1.4.20-1ubuntu3 grep_2.24-1 groff-base_1.22.3-7 gzip_1.6-4ubuntu1 help2man_1.47.3 hostname_3.16ubuntu2 init_1.29ubuntu1 init-system-helpers_1.29ubuntu1 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policyrcd-script-zg2_0.1-2 procps_2:3.3.10-4ubuntu2 readline-common_6.3-8ubuntu2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.2.2-7 sensible-utils_0.0.9 systemd_229-4ubuntu4 systemd-sysv_229-4ubuntu4 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.3ubuntu2 tar_1.28-2.1 tzdata_2016d-0ubuntu0.16.04 ubuntu-keyring_2012.05.19 util-linux_2.27.1-6ubuntu3 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu4 zlib1g-dev_1:1.2.8.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Format: 3.0 (quilt) Source: bamtools Binary: bamtools, libbamtools-dev, libbamtools2.4.0 Architecture: any Version: 2.4.0+dfsg-3build1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille , Kevin Murray , Dominique Belhachemi Homepage: https://github.com/pezmaster31/bamtools/wiki Standards-Version: 3.9.6 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bamtools.git Vcs-Git: git://anonscm.debian.org/debian-med/bamtools.git Build-Depends: debhelper (>= 9.0.0), d-shlibs (>= 0.56), cmake, zlib1g-dev, libjsoncpp-dev, help2man, doxygen Package-List: bamtools deb science optional arch=any libbamtools-dev deb libdevel optional arch=any libbamtools2.4.0 deb libs optional arch=any Checksums-Sha1: 17f2a562bb6fa95ba2b78a4bdab38a82fcc583d5 156628 bamtools_2.4.0+dfsg.orig.tar.xz 3cfb1be78a95df9bc6da5fa6016cd51bd39007b4 9752 bamtools_2.4.0+dfsg-3build1.debian.tar.xz Checksums-Sha256: 1f66a4971e70eac5c4aea6ee0c3e95d42af004b9578642b39812e7a552ea561d 156628 bamtools_2.4.0+dfsg.orig.tar.xz 2c071c1339ec97e07fbd45edad181a3b7378780c30b8d33c83ee44ecd8a5ec99 9752 bamtools_2.4.0+dfsg-3build1.debian.tar.xz Files: 8ee59abe9958df46f606af05691d5a2d 156628 bamtools_2.4.0+dfsg.orig.tar.xz 979d68e0727a8252a12e1dbc0f68e43d 9752 bamtools_2.4.0+dfsg-3build1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBAgAGBQJWucwQAAoJEAIZyhnQNDMM2+wH/jlTzEiSk+vfsZBYT6sripWz aVeh+NglkqaicNjSg6Hw9aOH6ogxi5NSrLCGiUKU40jBsd4rNdNjBIowajD0EeN7 p3AAbuzDXoYUiu1aCFlhQ75RGSPmpWcPq7PxwHkyEe6OKCgzHLFXFtnjHPfNSGUx HkT7Fo6NomKXolVXvWtBK6lZhAiBu8tElezNvRkqcf/d91SfUQt+oozNZfD23KHS kAqKjlojJDmzP3qRp0vpibDDX/R9VPL9MfzS0F6RNHo+bTA2YWFB0WdkA9+ezKZh IEIhdgNRMRBkLfRMpUAxxTS8QyU12yAOnK43Lh0eTGTTDRdGby7XN9yUb6DZrXI= =VN8a -----END PGP SIGNATURE----- gpgv: Signature made Tue Feb 9 11:22:56 2016 UTC using RSA key ID D034330C gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./bamtools_2.4.0+dfsg-3build1.dsc dpkg-source: info: extracting bamtools in /<> dpkg-source: info: unpacking bamtools_2.4.0+dfsg.orig.tar.xz dpkg-source: info: unpacking bamtools_2.4.0+dfsg-3build1.debian.tar.xz dpkg-source: info: applying 0001-ignore-thirdparty-and-fix-jsoncpp.patch dpkg-source: info: applying 0002-support-out-of-source-build.patch dpkg-source: info: applying 0003-remove-custom-ExportHeader-function-use-install-inst.patch dpkg-source: info: applying 0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch dpkg-source: info: applying 0006-Doxygen-reproducibility dpkg-source: info: applying 0006-Fix-Doxyfile-input-source-path.patch dpkg-source: info: applying 0007-Big_Endian.patch dpkg-source: info: applying 0008_Cmake_Test.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym 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-24758162 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-24758162 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-24758162 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: source package bamtools dpkg-buildpackage: source version 2.4.0+dfsg-3build1 dpkg-buildpackage: source distribution xenial dpkg-source --before-build bamtools-2.4.0+dfsg dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel dh_auto_clean -O--parallel dh_clean -O--parallel debian/rules build-arch dh build-arch --parallel dh_testdir -a -O--parallel dh_update_autotools_config -a -O--parallel dh_auto_configure -a -O--parallel cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -- The C compiler identification is GNU 5.3.1 -- The CXX compiler identification is GNU 5.3.1 -- Check for working C compiler: /usr/bin/arm-linux-gnueabihf-gcc -- Check for working C compiler: /usr/bin/arm-linux-gnueabihf-gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/arm-linux-gnueabihf-g++ -- Check for working CXX compiler: /usr/bin/arm-linux-gnueabihf-g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /<>/obj-arm-linux-gnueabihf debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build make -j4 make[2]: Entering directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -H/<> -B/<>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabihf/CMakeFiles /<>/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/depend make -f src/api/CMakeFiles/BamTools-static.dir/build.make src/api/CMakeFiles/BamTools-static.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/api /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/api /<>/obj-arm-linux-gnueabihf/src/api/CMakeFiles/BamTools.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/api /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/api /<>/obj-arm-linux-gnueabihf/src/api/CMakeFiles/BamTools-static.dir/DependInfo.cmake --color= Scanning dependencies of target BamTools-static Scanning dependencies of target BamTools make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/api/CMakeFiles/BamTools-static.dir/build.make src/api/CMakeFiles/BamTools-static.dir/build make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 1%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o [ 3%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o [ 3%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o [ 4%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o -c /<>/src/api/BamMultiReader.cpp cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -c /<>/src/api/BamMultiReader.cpp cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/BamAlignment.cpp.o -c /<>/src/api/BamAlignment.cpp cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o -c /<>/src/api/BamAlignment.cpp [ 5%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/BamReader.cpp.o -c /<>/src/api/BamReader.cpp [ 6%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/BamReader.cpp.o -c /<>/src/api/BamReader.cpp [ 7%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/BamWriter.cpp.o -c /<>/src/api/BamWriter.cpp [ 8%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/BamWriter.cpp.o -c /<>/src/api/BamWriter.cpp [ 9%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/SamHeader.cpp.o -c /<>/src/api/SamHeader.cpp [ 10%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamHeader.cpp.o -c /<>/src/api/SamHeader.cpp [ 11%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamProgram.cpp.o -c /<>/src/api/SamProgram.cpp [ 12%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/SamProgram.cpp.o -c /<>/src/api/SamProgram.cpp [ 13%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -c /<>/src/api/SamProgramChain.cpp [ 14%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o -c /<>/src/api/SamProgramChain.cpp [ 15%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o -c /<>/src/api/SamReadGroup.cpp [ 16%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -c /<>/src/api/SamReadGroup.cpp [ 17%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o -c /<>/src/api/SamReadGroupDictionary.cpp [ 18%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -c /<>/src/api/SamReadGroupDictionary.cpp [ 19%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/SamSequence.cpp.o -c /<>/src/api/SamSequence.cpp [ 20%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamSequence.cpp.o -c /<>/src/api/SamSequence.cpp [ 21%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -c /<>/src/api/SamSequenceDictionary.cpp [ 22%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o -c /<>/src/api/SamSequenceDictionary.cpp [ 23%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o -c /<>/src/api/internal/bam/BamHeader_p.cpp [ 24%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o -c /<>/src/api/internal/bam/BamHeader_p.cpp [ 25%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o -c /<>/src/api/internal/bam/BamMultiReader_p.cpp [ 26%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -c /<>/src/api/internal/bam/BamMultiReader_p.cpp [ 28%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o [ 28%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /<>/src/api/internal/bam/BamRandomAccessController_p.cpp cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /<>/src/api/internal/bam/BamRandomAccessController_p.cpp [ 29%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o -c /<>/src/api/internal/bam/BamReader_p.cpp [ 30%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -c /<>/src/api/internal/bam/BamReader_p.cpp [ 31%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o -c /<>/src/api/internal/bam/BamWriter_p.cpp [ 32%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -c /<>/src/api/internal/bam/BamWriter_p.cpp [ 33%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o -c /<>/src/api/internal/index/BamIndexFactory_p.cpp [ 34%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -c /<>/src/api/internal/index/BamIndexFactory_p.cpp [ 35%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o -c /<>/src/api/internal/index/BamStandardIndex_p.cpp [ 36%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -c /<>/src/api/internal/index/BamStandardIndex_p.cpp [ 37%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o -c /<>/src/api/internal/index/BamToolsIndex_p.cpp [ 38%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -c /<>/src/api/internal/index/BamToolsIndex_p.cpp [ 39%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o -c /<>/src/api/internal/io/BamDeviceFactory_p.cpp [ 40%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -c /<>/src/api/internal/io/BamDeviceFactory_p.cpp [ 41%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o -c /<>/src/api/internal/io/BamFile_p.cpp [ 42%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -c /<>/src/api/internal/io/BamFile_p.cpp [ 43%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o -c /<>/src/api/internal/io/BamFtp_p.cpp [ 44%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o -c /<>/src/api/internal/io/BamFtp_p.cpp [ 45%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o -c /<>/src/api/internal/io/BamHttp_p.cpp [ 46%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o -c /<>/src/api/internal/io/BamHttp_p.cpp [ 47%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o -c /<>/src/api/internal/io/BamPipe_p.cpp [ 48%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o -c /<>/src/api/internal/io/BamPipe_p.cpp [ 50%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o -c /<>/src/api/internal/io/BgzfStream_p.cpp [ 51%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -c /<>/src/api/internal/io/BgzfStream_p.cpp [ 52%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o -c /<>/src/api/internal/io/ByteArray_p.cpp [ 53%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -c /<>/src/api/internal/io/ByteArray_p.cpp [ 54%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o -c /<>/src/api/internal/io/HostAddress_p.cpp [ 55%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o -c /<>/src/api/internal/io/HostAddress_p.cpp [ 56%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o -c /<>/src/api/internal/io/HostInfo_p.cpp [ 57%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o -c /<>/src/api/internal/io/HostInfo_p.cpp [ 58%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o -c /<>/src/api/internal/io/HttpHeader_p.cpp [ 59%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o -c /<>/src/api/internal/io/ILocalIODevice_p.cpp [ 60%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o -c /<>/src/api/internal/io/HttpHeader_p.cpp [ 61%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -c /<>/src/api/internal/io/ILocalIODevice_p.cpp [ 62%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o -c /<>/src/api/internal/io/RollingBuffer_p.cpp [ 63%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -c /<>/src/api/internal/io/RollingBuffer_p.cpp [ 64%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o -c /<>/src/api/internal/io/TcpSocket_p.cpp [ 65%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o -c /<>/src/api/internal/io/TcpSocket_p.cpp [ 66%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o -c /<>/src/api/internal/io/TcpSocketEngine_p.cpp [ 67%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o -c /<>/src/api/internal/io/TcpSocketEngine_p.cpp [ 68%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o -c /<>/src/api/internal/io/TcpSocketEngine_unix_p.cpp [ 69%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o -c /<>/src/api/internal/sam/SamFormatParser_p.cpp [ 70%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o -c /<>/src/api/internal/io/TcpSocketEngine_unix_p.cpp [ 71%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /<>/src/api/internal/sam/SamFormatParser_p.cpp [ 72%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /<>/src/api/internal/sam/SamFormatPrinter_p.cpp [ 73%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /<>/src/api/internal/sam/SamFormatPrinter_p.cpp [ 74%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /<>/src/api/internal/sam/SamHeaderValidator_p.cpp [ 75%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /<>/src/api/internal/sam/SamHeaderValidator_p.cpp [ 76%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o -c /<>/src/api/internal/utils/BamException_p.cpp [ 77%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -fPIC -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /<>/src/api/internal/utils/BamException_p.cpp [ 78%] Linking CXX static library ../../lib/libbamtools.a cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/cmake -P CMakeFiles/BamTools-static.dir/cmake_clean_target.cmake cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools-static.dir/link.txt --verbose=1 [ 79%] Linking CXX shared library ../../lib/libbamtools.so cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libbamtools.a CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o CMakeFiles/BamTools-static.dir/BamReader.cpp.o CMakeFiles/BamTools-static.dir/BamWriter.cpp.o CMakeFiles/BamTools-static.dir/SamHeader.cpp.o CMakeFiles/BamTools-static.dir/SamProgram.cpp.o CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools-static.dir/SamSequence.cpp.o CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o /usr/bin/ranlib ../../lib/libbamtools.a /usr/bin/arm-linux-gnueabihf-g++ -fPIC -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libbamtools.so.2.4.0 -o ../../lib/libbamtools.so.2.4.0 CMakeFiles/BamTools.dir/BamAlignment.cpp.o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o CMakeFiles/BamTools.dir/BamReader.cpp.o CMakeFiles/BamTools.dir/BamWriter.cpp.o CMakeFiles/BamTools.dir/SamHeader.cpp.o CMakeFiles/BamTools.dir/SamProgram.cpp.o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools.dir/SamSequence.cpp.o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -lz make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 79%] Built target BamTools-static cd /<>/obj-arm-linux-gnueabihf/src/api && /usr/bin/cmake -E cmake_symlink_library ../../lib/libbamtools.so.2.4.0 ../../lib/libbamtools.so.2.4.0 ../../lib/libbamtools.so make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 79%] Built target BamTools make -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/utils /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/utils /<>/obj-arm-linux-gnueabihf/src/utils/CMakeFiles/BamTools-utils.dir/DependInfo.cmake --color= Scanning dependencies of target BamTools-utils make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o [ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o [ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o [ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/utils && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_UTILS_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o -c /<>/src/utils/bamtools_pileup_engine.cpp cd /<>/obj-arm-linux-gnueabihf/src/utils && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_UTILS_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o -c /<>/src/utils/bamtools_fasta.cpp cd /<>/obj-arm-linux-gnueabihf/src/utils && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_UTILS_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o -c /<>/src/utils/bamtools_utilities.cpp cd /<>/obj-arm-linux-gnueabihf/src/utils && /usr/bin/arm-linux-gnueabihf-g++ -DBAMTOOLS_UTILS_LIBRARY -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -fPIC -o CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o -c /<>/src/utils/bamtools_options.cpp [ 84%] Linking CXX static library ../../lib/libbamtools-utils.a cd /<>/obj-arm-linux-gnueabihf/src/utils && /usr/bin/cmake -P CMakeFiles/BamTools-utils.dir/cmake_clean_target.cmake cd /<>/obj-arm-linux-gnueabihf/src/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools-utils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libbamtools-utils.a CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o /usr/bin/ranlib ../../lib/libbamtools-utils.a make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 84%] Built target BamTools-utils make -f src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make src/toolkit/CMakeFiles/bamtools_cmd.dir/depend make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/toolkit /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/toolkit /<>/obj-arm-linux-gnueabihf/src/toolkit/CMakeFiles/bamtools_cmd.dir/DependInfo.cmake --color= Scanning dependencies of target bamtools_cmd make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make src/toolkit/CMakeFiles/bamtools_cmd.dir/build make[4]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 85%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/arm-linux-gnueabihf-g++ -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -I/<>/src/utils -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o -c /<>/src/toolkit/bamtools_filter.cpp [ 86%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o [ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/arm-linux-gnueabihf-g++ -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -I/<>/src/utils -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o -c /<>/src/toolkit/bamtools_convert.cpp cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/arm-linux-gnueabihf-g++ -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -I/<>/src/utils -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o -c /<>/src/toolkit/bamtools_count.cpp [ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/arm-linux-gnueabihf-g++ -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -I/<>/src/utils -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o -c /<>/src/toolkit/bamtools_coverage.cpp /<>/src/toolkit/bamtools_filter.cpp: In member function ‘bool BamTools::FilterTool::FilterToolPrivate::ParseScript()’: /<>/src/toolkit/bamtools_filter.cpp:650:50: warning: ‘std::__cxx11::string Json::Reader::getFormatedErrorMessages() const’ is deprecated: Use getFormattedErrorMessages() instead. [-Wdeprecated-declarations] << reader.getFormatedErrorMessages(); ^ In file included from /usr/include/jsoncpp/json/json.h:11:0, from /<>/src/toolkit/bamtools_filter.cpp:19: /usr/include/jsoncpp/json/reader.h:114:18: note: declared here JSONCPP_STRING getFormatedErrorMessages() const; ^ [ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/arm-linux-gnueabihf-g++ -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -I/<>/src/utils -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o -c /<>/src/toolkit/bamtools_header.cpp [ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/arm-linux-gnueabihf-g++ -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -I/<>/src/utils -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o -c /<>/src/toolkit/bamtools_index.cpp [ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/arm-linux-gnueabihf-g++ -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -I/<>/src/utils -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o -c /<>/src/toolkit/bamtools_merge.cpp [ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/arm-linux-gnueabihf-g++ -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -I/<>/src/utils -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o -c /<>/src/toolkit/bamtools_random.cpp [ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/arm-linux-gnueabihf-g++ -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -I/<>/src/utils -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o -c /<>/src/toolkit/bamtools_resolve.cpp [ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/arm-linux-gnueabihf-g++ -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -I/<>/src/utils -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o -c /<>/src/toolkit/bamtools_revert.cpp [ 95%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/arm-linux-gnueabihf-g++ -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -I/<>/src/utils -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o -c /<>/src/toolkit/bamtools_sort.cpp [ 96%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/arm-linux-gnueabihf-g++ -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -I/<>/src/utils -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o -c /<>/src/toolkit/bamtools_split.cpp [ 97%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/arm-linux-gnueabihf-g++ -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -I/<>/src/utils -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o -c /<>/src/toolkit/bamtools_stats.cpp [ 98%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/arm-linux-gnueabihf-g++ -D_FILE_OFFSET_BITS=64 -I/<>/src -I/<>/obj-arm-linux-gnueabihf/include -I/<>/src/api -I/<>/src/utils -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -c /<>/src/toolkit/bamtools.cpp [100%] Linking CXX executable ../../bin/bamtools cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/bamtools_cmd.dir/link.txt --verbose=1 /usr/bin/arm-linux-gnueabihf-g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -o ../../bin/bamtools-2.4.0 -rdynamic ../../lib/libbamtools-utils.a -ljsoncpp ../../lib/libbamtools.so.2.4.0 -lz -Wl,-rpath,/<>/obj-arm-linux-gnueabihf/lib: cd /<>/obj-arm-linux-gnueabihf/src/toolkit && /usr/bin/cmake -E cmake_symlink_executable ../../bin/bamtools-2.4.0 ../../bin/bamtools make[4]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [100%] Built target bamtools_cmd make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabihf/CMakeFiles 0 make[2]: Leaving directory '/<>/obj-arm-linux-gnueabihf' doxygen docs/Doxyfile warning: Tag `SYMBOL_CACHE_SIZE' at line 300 of file `docs/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `SHOW_DIRECTORIES' at line 500 of file `docs/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `HTML_ALIGN_MEMBERS' at line 862 of file `docs/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `USE_INLINE_TREES' at line 1032 of file `docs/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `XML_SCHEMA' at line 1244 of file `docs/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `XML_DTD' at line 1250 of file `docs/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: doxygen no longer ships with the FreeSans font. You may want to clear or change DOT_FONTNAME. Otherwise you run the risk that the wrong font is being used for dot generated graphs. /<>/src/api/BamAlignment.h:174: warning: found \endinternal without matching \internal Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching for files in directory /<>/src/api/internal Searching for files in directory /<>/src/api/internal/bam Searching for files in directory /<>/src/api/internal/index Searching for files in directory /<>/src/api/internal/io Searching for files in directory /<>/src/api/internal/sam Searching for files in directory /<>/src/api/internal/utils Searching INPUT for files to process... Searching for files in directory /<>/src/api Searching for files in directory /<>/src/api/algorithms Searching for files in directory /<>/src/api/internal Searching for files in directory /<>/src/api/internal/bam Searching for files in directory /<>/src/api/internal/index Searching for files in directory /<>/src/api/internal/io Searching for files in directory /<>/src/api/internal/sam Searching for files in directory /<>/src/api/internal/utils Reading and parsing tag files Parsing files Preprocessing /<>/src/api/algorithms/Sort.h... Parsing file /<>/src/api/algorithms/Sort.h... Preprocessing /<>/src/api/api_global.h... Parsing file /<>/src/api/api_global.h... Preprocessing /<>/src/api/BamAlgorithms.h... Parsing file /<>/src/api/BamAlgorithms.h... Preprocessing /<>/src/api/BamAlignment.cpp... Parsing file /<>/src/api/BamAlignment.cpp... Preprocessing /<>/src/api/BamAlignment.h... Parsing file /<>/src/api/BamAlignment.h... Preprocessing /<>/src/api/BamAux.h... Parsing file /<>/src/api/BamAux.h... Preprocessing /<>/src/api/BamConstants.h... Parsing file /<>/src/api/BamConstants.h... Preprocessing /<>/src/api/BamIndex.h... Parsing file /<>/src/api/BamIndex.h... Preprocessing /<>/src/api/BamMultiReader.cpp... Parsing file /<>/src/api/BamMultiReader.cpp... Preprocessing /<>/src/api/BamMultiReader.h... Parsing file /<>/src/api/BamMultiReader.h... Preprocessing /<>/src/api/BamReader.cpp... Parsing file /<>/src/api/BamReader.cpp... Preprocessing /<>/src/api/BamReader.h... Parsing file /<>/src/api/BamReader.h... Preprocessing /<>/src/api/BamWriter.cpp... Parsing file /<>/src/api/BamWriter.cpp... Preprocessing /<>/src/api/BamWriter.h... Parsing file /<>/src/api/BamWriter.h... Preprocessing /<>/src/api/IBamIODevice.h... Parsing file /<>/src/api/IBamIODevice.h... Preprocessing /<>/src/api/BamMultiReader.cpp:26: warning: Documentation for undefined enum `MergeOrder' found. /<>/src/api/BamAlignment.h:180: warning: documented symbol `bool BamTools::AddTag' was not declared or defined. /<>/src/api/BamAlignment.h:290: warning: documented symbol `template< typename T > bool BamTools::AddTag' was not declared or defined. /<>/src/api/BamAlignment.h:356: warning: documented symbol `template< typename T > bool BamTools::EditTag' was not declared or defined. /<>/src/api/BamAlignment.h:383: warning: documented symbol `template< typename T > bool BamTools::EditTag' was not declared or defined. /<>/src/api/BamAlignment.h:408: warning: documented symbol `template< typename T > bool BamTools::GetTag' was not declared or defined. /<>/src/api/BamAlignment.h:532: warning: documented symbol `template< typename T > bool BamTools::GetTag' was not declared or defined. /<>/src/api/SamConstants.h... Parsing file /<>/src/api/SamConstants.h... Preprocessing /<>/src/api/SamHeader.cpp... Parsing file /<>/src/api/SamHeader.cpp... Preprocessing /<>/src/api/SamHeader.h... Parsing file /<>/src/api/SamHeader.h... Preprocessing /<>/src/api/SamProgram.cpp... Parsing file /<>/src/api/SamProgram.cpp... Preprocessing /<>/src/api/SamProgram.h... Parsing file /<>/src/api/SamProgram.h... Preprocessing /<>/src/api/SamProgramChain.cpp... Parsing file /<>/src/api/SamProgramChain.cpp... Preprocessing /<>/src/api/SamProgramChain.h... Parsing file /<>/src/api/SamProgramChain.h... Preprocessing /<>/src/api/SamReadGroup.cpp... Parsing file /<>/src/api/SamReadGroup.cpp... Preprocessing /<>/src/api/SamReadGroup.h... Parsing file /<>/src/api/SamReadGroup.h... Preprocessing /<>/src/api/SamReadGroupDictionary.cpp... Parsing file /<>/src/api/SamReadGroupDictionary.cpp... Preprocessing /<>/src/api/SamReadGroupDictionary.h... Parsing file /<>/src/api/SamReadGroupDictionary.h... Preprocessing /<>/src/api/SamSequence.cpp... Parsing file /<>/src/api/SamSequence.cpp... Preprocessing /<>/src/api/SamSequence.h... Parsing file /<>/src/api/SamSequence.h... Preprocessing /<>/src/api/SamSequenceDictionary.cpp... Parsing file /<>/src/api/SamSequenceDictionary.cpp... Preprocessing /<>/src/api/SamSequenceDictionary.h... Parsing file /<>/src/api/SamSequenceDictionary.h... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Associating documentation with classes... Computing nesting relations for classes... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Creating members for template instances... Computing class relations... Add enum values to enums... Searching for member function documentation... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Freeing entry tree Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Computing dependencies between directories... Generating citations page... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations../<>/src/api/BamMultiReader.cpp:362: warning: Found unknown command `\bold' /<>/src/api/BamMultiReader.cpp:365: warning: Found unknown command `\bold' . Adding members to index pages... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file api_global.h... Generating code for file BamAlgorithms.h... Generating code for file BamAlignment.h... Generating code for file BamAux.h... Generating code for file BamConstants.h... Generating code for file BamIndex.h... Generating code for file BamMultiReader.h... Generating code for file BamReader.h... Generating code for file BamWriter.h... Generating code for file IBamIODevice.h... Generating code for file SamConstants.h... Generating code for file SamHeader.h... Generating code for file SamProgram.h... Generating code for file SamProgramChain.h... Generating code for file SamReadGroup.h... Generating code for file SamReadGroupDictionary.h... Generating code for file SamSequence.h... Generating code for file SamSequenceDictionary.h... Generating code for file Sort.h... Generating file documentation... Generating docs for file api_global.h... Generating docs for file BamAlgorithms.h... Generating docs for file BamAlignment.cpp... Generating docs for file BamAlignment.h... Generating docs for file BamAux.h... Generating docs for file BamConstants.h... Generating docs for file BamIndex.h... Generating docs for file BamMultiReader.cpp... Generating docs for file BamMultiReader.h... Generating docs for file BamReader.cpp... Generating docs for file BamReader.h... Generating docs for file BamWriter.cpp... Generating docs for file BamWriter.h... Generating docs for file IBamIODevice.h... Generating docs for file SamConstants.h... Generating docs for file SamHeader.cpp... Generating docs for file SamHeader.h... Generating docs for file SamProgram.cpp... Generating docs for file SamProgram.h... Generating docs for file SamProgramChain.cpp... Generating docs for file SamProgramChain.h... Generating docs for file SamReadGroup.cpp... Generating docs for file SamReadGroup.h... Generating docs for file SamReadGroupDictionary.cpp... Generating docs for file SamReadGroupDictionary.h... Generating docs for file SamSequence.cpp... Generating docs for file SamSequence.h... Generating docs for file SamSequenceDictionary.cpp... Generating docs for file SamSequenceDictionary.h... Generating docs for file Sort.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating namespace index... Generating docs for namespace BamTools Generating docs for compound BamTools::BamAlignment... Generating docs for compound BamTools::BamIndex... Generating docs for compound BamTools::BamMultiReader... Generating docs for compound BamTools::BamReader... Generating docs for compound BamTools::BamRegion... Generating docs for compound BamTools::BamWriter... Generating docs for compound BamTools::CigarOp... Generating docs for compound BamTools::CustomHeaderTag... Generating docs for compound BamTools::IBamIODevice... Generating docs for compound BamTools::RefData... Generating docs for compound BamTools::SamHeader... Generating docs for compound BamTools::SamProgram... Generating docs for compound BamTools::SamProgramChain... Generating docs for compound BamTools::SamReadGroup... Generating docs for compound BamTools::SamReadGroupDictionary... Generating docs for compound BamTools::SamSequence... Generating docs for compound BamTools::SamSequenceDictionary... Generating docs for namespace BamTools::Algorithms Generating docs for compound BamTools::Algorithms::Sort... Generating docs for nested compound BamTools::Algorithms::Sort::ByName... Generating docs for nested compound BamTools::Algorithms::Sort::ByPosition... Generating docs for nested compound BamTools::Algorithms::Sort::ByTag... Generating docs for nested compound BamTools::Algorithms::Sort::Unsorted... Generating docs for namespace BamTools::Constants Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... lookup cache used 1198/65536 hits=6250 misses=1229 finished... make[1]: Leaving directory '/<>' dh_auto_test -a -O--parallel make -j4 test ARGS\+=-j4 make[1]: Entering directory '/<>/obj-arm-linux-gnueabihf' Running tests... /usr/bin/ctest --force-new-ctest-process -j4 Test project /<>/obj-arm-linux-gnueabihf Start 1: bamtools_help Start 2: bamtools_stats 1/2 Test #1: bamtools_help .................... Passed 0.01 sec 2/2 Test #2: bamtools_stats ................... Passed 0.01 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 0.02 sec make[1]: Leaving directory '/<>/obj-arm-linux-gnueabihf' fakeroot debian/rules binary-arch dh binary-arch --parallel dh_testroot -a -O--parallel dh_prep -a -O--parallel dh_auto_install -a -O--parallel make -j4 install DESTDIR=/<>/bamtools-2.4.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -H/<> -B/<>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabihf/CMakeFiles /<>/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-arm-linux-gnueabihf' make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/depend make -f src/api/CMakeFiles/BamTools-static.dir/build.make src/api/CMakeFiles/BamTools-static.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/api /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/api /<>/obj-arm-linux-gnueabihf/src/api/CMakeFiles/BamTools.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/api /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/api /<>/obj-arm-linux-gnueabihf/src/api/CMakeFiles/BamTools-static.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/build make -f src/api/CMakeFiles/BamTools-static.dir/build.make src/api/CMakeFiles/BamTools-static.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'src/api/CMakeFiles/BamTools.dir/build'. make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'src/api/CMakeFiles/BamTools-static.dir/build'. make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 55%] Built target BamTools [ 79%] Built target BamTools-static make -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/utils /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/utils /<>/obj-arm-linux-gnueabihf/src/utils/CMakeFiles/BamTools-utils.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'src/utils/CMakeFiles/BamTools-utils.dir/build'. make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 84%] Built target BamTools-utils make -f src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make src/toolkit/CMakeFiles/bamtools_cmd.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/toolkit /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/toolkit /<>/obj-arm-linux-gnueabihf/src/toolkit/CMakeFiles/bamtools_cmd.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make src/toolkit/CMakeFiles/bamtools_cmd.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'src/toolkit/CMakeFiles/bamtools_cmd.dir/build'. make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [100%] Built target bamtools_cmd make[2]: Leaving directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabihf/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /<>/debian/tmp/usr/include/bamtools/shared/bamtools_global.h -- Installing: /<>/debian/tmp/usr/lib/libbamtools.so.2.4.0 -- Installing: /<>/debian/tmp/usr/lib/libbamtools.so -- Installing: /<>/debian/tmp/usr/lib/libbamtools.a -- Installing: /<>/debian/tmp/usr/include/bamtools/api/api_global.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/BamAlgorithms.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/BamAlignment.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/BamAux.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/BamConstants.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/BamIndex.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/BamMultiReader.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/BamReader.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/BamWriter.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/IBamIODevice.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/SamConstants.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/SamHeader.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/SamProgram.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/SamProgramChain.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/SamReadGroup.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/SamReadGroupDictionary.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/SamSequence.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/SamSequenceDictionary.h -- Installing: /<>/debian/tmp/usr/include/bamtools/api/algorithms/Sort.h -- Installing: /<>/debian/tmp/usr/include/bamtools/bamtools_version.h -- Installing: /<>/debian/tmp/usr/bin/bamtools-2.4.0 -- Installing: /<>/debian/tmp/usr/bin/bamtools -- Set runtime path of "/<>/debian/tmp/usr/bin/bamtools-2.4.0" to "" make[1]: Leaving directory '/<>/obj-arm-linux-gnueabihf' debian/rules override_dh_install make[1]: Entering directory '/<>' d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include/* usr/include \ debian/tmp/usr/lib/lib*.so Library package automatic movement utility --> zlib1g-dev package exists. set -e install -d -m 755 debian/libbamtools-dev/usr/lib/arm-linux-gnueabihf install -d -m 755 debian/libbamtools2.4.0/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/libbamtools.a debian/libbamtools-dev/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/libbamtools.so debian/libbamtools-dev/usr/lib/arm-linux-gnueabihf mv /<>/debian/tmp/usr/lib/libbamtools.so.2.4.0 debian/libbamtools2.4.0/usr/lib/arm-linux-gnueabihf PKGDEV=libbamtools-dev PKGSHL=libbamtools2.4.0 install -d -m 755 debian/libbamtools-dev/usr/include mv debian/tmp/usr/include/bamtools debian/libbamtools-dev/usr/include dh_install # no need to install different versions of bamtools rm -rf debian/bamtools/usr/bin/bamtools mv debian/bamtools/usr/bin/bamtools-[0-9]* debian/bamtools/usr/bin/bamtools rm -f debian/libbamtools-dev/usr/share/doc/libbamtools-dev/html/jquery.js ln -s /usr/share/javascript/jquery/jquery.js debian/libbamtools-dev/usr/share/doc/libbamtools-dev/html/jquery.js make[1]: Leaving directory '/<>' dh_installdocs -a -O--parallel dh_installchangelogs -a -O--parallel dh_installman -a -O--parallel dh_lintian -a -O--parallel dh_perl -a -O--parallel dh_link -a -O--parallel dh_strip_nondeterminism -a -O--parallel dh_compress -a -O--parallel dh_fixperms -a -O--parallel dh_strip -a -O--parallel dh_strip debug symbol extraction: not enabling -a because /CurrentlyBuilding exists dh_strip debug symbol extraction: all non-arch-all packages for this build platform armhf: bamtools libbamtools-dev libbamtools2.4.0 dh_strip debug symbol extraction: packages to act on: bamtools libbamtools-dev libbamtools2.4.0 dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol Using buildid for compat level >= 9 libbamtools-dev has no unstripped objects, ignoring find: ‘/<>/debian/libbamtools-dev-dbgsym’: No such file or directory /usr/bin/pkg_create_dbgsym: nothing in /<>/debian/libbamtools-dev-dbgsym and no dbgdepends, ignoring Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol dh_makeshlibs -a -O--parallel dh_shlibdeps -a -O--parallel dpkg-shlibdeps: warning: debian/bamtools/usr/bin/bamtools contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/bamtools/usr/bin/bamtools was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols) dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libbamtools2.4.0/usr/lib/arm-linux-gnueabihf/libbamtools.so.2.4.0 found in none of the libraries dh_installdeb -a -O--parallel dh_gencontrol -a -O--parallel dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package libbamtools-dev: unused substitution variable ${devlibs:Depends} dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform armhf: bamtools libbamtools-dev libbamtools2.4.0 dh_gencontrol debug symbol wrapper: packages to act on: bamtools libbamtools-dev libbamtools2.4.0 dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package bamtools (pkgdir debian/bamtools, ddeb package dir debian/bamtools-dbgsym) dh_gencontrol debug symbol wrapper: building bamtools-dbgsym_2.4.0+dfsg-3build1_armhf.ddeb dpkg-deb: building package 'bamtools-dbgsym' in '../bamtools-dbgsym_2.4.0+dfsg-3build1_armhf.ddeb'. dh_gencontrol debug symbol wrapper: no debian/libbamtools-dev-dbgsym, skipping package libbamtools-dev dh_gencontrol debug symbol wrapper: processing package libbamtools2.4.0 (pkgdir debian/libbamtools2.4.0, ddeb package dir debian/libbamtools2.4.0-dbgsym) dh_gencontrol debug symbol wrapper: building libbamtools2.4.0-dbgsym_2.4.0+dfsg-3build1_armhf.ddeb dpkg-deb: building package 'libbamtools2.4.0-dbgsym' in '../libbamtools2.4.0-dbgsym_2.4.0+dfsg-3build1_armhf.ddeb'. dh_md5sums -a -O--parallel dh_builddeb -a -O--parallel INFO: pkgstriptranslations version 129 INFO: pkgstriptranslations version 129 INFO: pkgstriptranslations version 129 pkgstriptranslations: processing libbamtools-dev (in debian/libbamtools-dev); do_strip: , oemstrip: pkgstriptranslations: processing libbamtools2.4.0 (in debian/libbamtools2.4.0); do_strip: , oemstrip: pkgstriptranslations: processing bamtools (in debian/bamtools); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libbamtools-dev/DEBIAN/control, package libbamtools-dev, directory debian/libbamtools-dev INFO: pkgstripfiles: waiting for lock (libbamtools-dev) ... INFO: pkgstripfiles: waiting for lock (libbamtools-dev) ... INFO: pkgstripfiles: waiting for lock (libbamtools-dev) ... INFO: pkgstripfiles: waiting for lock (libbamtools-dev) ... INFO: pkgstripfiles: waiting for lock (libbamtools-dev) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/bamtools/DEBIAN/control, package bamtools, directory debian/bamtools Searching for duplicated docs in dependency libbamtools2.4.0... symlinking changelog.Debian.gz in bamtools to file in libbamtools2.4.0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package bamtools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'bamtools' in '../bamtools_2.4.0+dfsg-3build1_armhf.deb'. Searching for duplicated docs in dependency libbamtools2.4.0... symlinking changelog.Debian.gz in libbamtools-dev to file in libbamtools2.4.0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libbamtools-dev ... oooooooooooooooooooooooo. pkgstripfiles: PNG optimization (24/0) for package libbamtools-dev took 1 s dpkg-deb: building package 'libbamtools-dev' in '../libbamtools-dev_2.4.0+dfsg-3build1_armhf.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libbamtools2.4.0/DEBIAN/control, package libbamtools2.4.0, directory debian/libbamtools2.4.0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libbamtools2.4.0 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libbamtools2.4.0' in '../libbamtools2.4.0_2.4.0+dfsg-3build1_armhf.deb'. dpkg-genchanges -B -mLaunchpad Build Daemon >../bamtools_2.4.0+dfsg-3build1_armhf.changes dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build bamtools-2.4.0+dfsg dpkg-buildpackage: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-12-03T11:12:26Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bamtools_2.4.0+dfsg-3build1_armhf.changes: ------------------------------------------ Format: 1.8 Date: Tue, 09 Feb 2016 12:21:15 +0100 Source: bamtools Binary: bamtools libbamtools-dev libbamtools2.4.0 Architecture: armhf Version: 2.4.0+dfsg-3build1 Distribution: xenial Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Łukasz 'sil2100' Zemczak Description: bamtools - toolkit for manipulating BAM (genome alignment) files libbamtools-dev - C++ API for manipulating BAM (genome alignment) files libbamtools2.4.0 - dynamic library for manipulating BAM (genome alignment) files Changes: bamtools (2.4.0+dfsg-3build1) xenial; urgency=medium . * No-change rebuild for the libjsoncpp transition. Checksums-Sha1: 9673a08410847f8d48ab92d43afd44a6f6170621 168680 bamtools_2.4.0+dfsg-3build1_armhf.deb 79afa13b0a76e6303f4ede633266ae3be15625ad 363272 libbamtools-dev_2.4.0+dfsg-3build1_armhf.deb b11d36bc4145f48fcb2c387e3538de529b7ccd05 166244 libbamtools2.4.0_2.4.0+dfsg-3build1_armhf.deb Checksums-Sha256: dbcac8acbf4e26feed3735cda8dd098f6ed5dd077244611c54ded361cfc4e51b 168680 bamtools_2.4.0+dfsg-3build1_armhf.deb c39d56c3d2c46cba29458435a8d4e68dde4c7ad498003b965f532dafc86b06b9 363272 libbamtools-dev_2.4.0+dfsg-3build1_armhf.deb 42f5e9edbf6cd44224c45788d61843a52cdb4b99af45489de82771c1d498a823 166244 libbamtools2.4.0_2.4.0+dfsg-3build1_armhf.deb Files: 378f55ebc72a2165df75b083a6d0d45c 168680 science optional bamtools_2.4.0+dfsg-3build1_armhf.deb 6f7789e24ba3449b3f7c51ae7bb6013d 363272 libdevel optional libbamtools-dev_2.4.0+dfsg-3build1_armhf.deb 44f7791ab08b737121f1046b73097016 166244 libs optional libbamtools2.4.0_2.4.0+dfsg-3build1_armhf.deb /<>/bamtools_2.4.0+dfsg-3build1_armhf.changes.new could not be renamed to /<>/bamtools_2.4.0+dfsg-3build1_armhf.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bamtools_2.4.0+dfsg-3build1_armhf.deb ------------------------------------- new debian package, version 2.0. size 168680 bytes: control archive=1304 bytes. 1865 bytes, 38 lines control 256 bytes, 4 lines md5sums Package: bamtools Version: 2.4.0+dfsg-3build1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 399 Depends: libbamtools2.4.0, libc6 (>= 2.4), libgcc1 (>= 1:3.5), libjsoncpp1, libstdc++6 (>= 5.2) Section: science Priority: optional Homepage: https://github.com/pezmaster31/bamtools/wiki Description: toolkit for manipulating BAM (genome alignment) files BamTools facilitates research analysis and data management using BAM files. It copes with the enormous amount of data produced by current sequencing technologies that is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. . BamTools provides both a C++ API for BAM file support as well as a command-line toolkit. . This is the bamtools command-line toolkit. . Available bamtools commands: convert Converts between BAM and a number of other formats count Prints number of alignments in BAM file(s) coverage Prints coverage statistics from the input BAM file filter Filters BAM file(s) by user-specified criteria header Prints BAM header information index Generates index for BAM file merge Merge multiple BAM files into single file random Select random alignments from existing BAM file(s), intended more as a testing tool. resolve Resolves paired-end reads (marking the IsProperPair flag as needed) revert Removes duplicate marks and restores original base qualities sort Sorts the BAM file according to some criteria split Splits a BAM file on user-specified property, creating a new BAM output file for each value found stats Prints some basic statistics from input BAM file(s) drwxr-xr-x root/root 0 2022-12-03 11:11 ./ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/bin/ -rwxr-xr-x root/root 391736 2022-12-03 11:11 ./usr/bin/bamtools drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/share/ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-12-03 11:12 ./usr/share/doc/bamtools/ lrwxrwxrwx root/root 0 2022-12-03 11:12 ./usr/share/doc/bamtools/changelog.Debian.gz -> ../libbamtools2.4.0/changelog.Debian.gz -rw-r--r-- root/root 1665 2015-12-20 21:15 ./usr/share/doc/bamtools/copyright drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/share/lintian/ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 71 2015-12-20 20:37 ./usr/share/lintian/overrides/bamtools drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/share/man/ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/share/man/man1/ -rw-r--r-- root/root 792 2022-12-03 11:11 ./usr/share/man/man1/bamtools.1.gz libbamtools-dev_2.4.0+dfsg-3build1_armhf.deb -------------------------------------------- new debian package, version 2.0. size 363272 bytes: control archive=11136 bytes. 936 bytes, 22 lines control 37108 bytes, 403 lines md5sums Package: libbamtools-dev Source: bamtools Version: 2.4.0+dfsg-3build1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3938 Depends: libbamtools2.4.0 (= 2.4.0+dfsg-3build1) Section: libdevel Priority: optional Homepage: https://github.com/pezmaster31/bamtools/wiki Description: C++ API for manipulating BAM (genome alignment) files BamTools facilitates research analysis and data management using BAM files. It copes with the enormous amount of data produced by current sequencing technologies that is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. . BamTools provides both a C++ API for BAM file support as well as a command-line toolkit. . This is the developers API package. drwxr-xr-x root/root 0 2022-12-03 11:11 ./ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/include/ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/include/bamtools/ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/include/bamtools/api/ -rw-r--r-- root/root 847 2015-06-16 16:50 ./usr/include/bamtools/api/BamAlgorithms.h -rw-r--r-- root/root 23756 2015-06-16 16:50 ./usr/include/bamtools/api/BamAlignment.h -rw-r--r-- root/root 14867 2022-12-03 11:09 ./usr/include/bamtools/api/BamAux.h -rw-r--r-- root/root 9682 2015-06-16 16:50 ./usr/include/bamtools/api/BamConstants.h -rw-r--r-- root/root 2885 2015-06-16 16:50 ./usr/include/bamtools/api/BamIndex.h -rw-r--r-- root/root 4676 2015-06-16 16:50 ./usr/include/bamtools/api/BamMultiReader.h -rw-r--r-- root/root 4285 2015-06-16 16:50 ./usr/include/bamtools/api/BamReader.h -rw-r--r-- root/root 2208 2015-06-16 16:50 ./usr/include/bamtools/api/BamWriter.h -rw-r--r-- root/root 3022 2015-06-16 16:50 ./usr/include/bamtools/api/IBamIODevice.h -rw-r--r-- root/root 3725 2015-06-16 16:50 ./usr/include/bamtools/api/SamConstants.h -rw-r--r-- root/root 2959 2015-06-16 16:50 ./usr/include/bamtools/api/SamHeader.h -rw-r--r-- root/root 2389 2015-06-16 16:50 ./usr/include/bamtools/api/SamProgram.h -rw-r--r-- root/root 3127 2015-06-16 16:50 ./usr/include/bamtools/api/SamProgramChain.h -rw-r--r-- root/root 3449 2015-06-16 16:50 ./usr/include/bamtools/api/SamReadGroup.h -rw-r--r-- root/root 3281 2015-06-16 16:50 ./usr/include/bamtools/api/SamReadGroupDictionary.h -rw-r--r-- root/root 2567 2015-06-16 16:50 ./usr/include/bamtools/api/SamSequence.h -rw-r--r-- root/root 3248 2015-06-16 16:50 ./usr/include/bamtools/api/SamSequenceDictionary.h drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/include/bamtools/api/algorithms/ -rw-r--r-- root/root 12112 2015-06-16 16:50 ./usr/include/bamtools/api/algorithms/Sort.h -rw-r--r-- root/root 757 2015-06-16 16:50 ./usr/include/bamtools/api/api_global.h -rw-r--r-- root/root 852 2022-12-03 11:09 ./usr/include/bamtools/bamtools_version.h drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/include/bamtools/shared/ -rw-r--r-- root/root 2790 2015-06-16 16:50 ./usr/include/bamtools/shared/bamtools_global.h drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/lib/ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/lib/arm-linux-gnueabihf/ -rw-r--r-- root/root 880108 2022-12-03 11:11 ./usr/lib/arm-linux-gnueabihf/libbamtools.a lrwxrwxrwx root/root 0 2022-12-03 11:11 ./usr/lib/arm-linux-gnueabihf/libbamtools.so -> libbamtools.so.2.4.0 drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/share/ drwxr-xr-x root/root 0 2015-12-20 20:37 ./usr/share/cmake/ drwxr-xr-x root/root 0 2015-12-20 20:37 ./usr/share/cmake/bamtools/ -rw-r--r-- root/root 1574 2015-12-20 20:37 ./usr/share/cmake/bamtools/bamtools-config.cmake drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/share/doc-base/ -rw-r--r-- root/root 325 2015-12-20 20:37 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libbamtools2.4.0 Source: bamtools Version: 2.4.0+dfsg-3build1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 383 Depends: libc6 (>= 2.15), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4) Section: libs Priority: optional Homepage: https://github.com/pezmaster31/bamtools/wiki Description: dynamic library for manipulating BAM (genome alignment) files BamTools facilitates research analysis and data management using BAM files. It copes with the enormous amount of data produced by current sequencing technologies that is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. . BamTools provides both a C++ API for BAM file support as well as a command-line toolkit. . This is the runtime library. drwxr-xr-x root/root 0 2022-12-03 11:11 ./ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/lib/ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/lib/arm-linux-gnueabihf/ -rw-r--r-- root/root 374864 2022-12-03 11:11 ./usr/lib/arm-linux-gnueabihf/libbamtools.so.2.4.0 drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/share/ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/share/doc/libbamtools2.4.0/ -rw-r--r-- root/root 933 2016-02-09 11:22 ./usr/share/doc/libbamtools2.4.0/changelog.Debian.gz -rw-r--r-- root/root 1665 2015-12-20 21:15 ./usr/share/doc/libbamtools2.4.0/copyright drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/share/lintian/ drwxr-xr-x root/root 0 2022-12-03 11:11 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 100 2015-12-20 20:37 ./usr/share/lintian/overrides/libbamtools2.4.0 +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: 96064 Build-Time: 164 Distribution: xenial Host Architecture: armhf Install-Time: 18 Job: bamtools_2.4.0+dfsg-3build1.dsc Machine Architecture: arm64 Package: bamtools Package-Time: 186 Source-Version: 2.4.0+dfsg-3build1 Space: 96064 Status: successful Version: 2.4.0+dfsg-3build1 -------------------------------------------------------------------------------- Finished at 2022-12-03T11:12:26Z Build needed 00:03:06, 96064k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=xenial --arch=armhf PACKAGEBUILD-24758162 Scanning for processes to kill in build PACKAGEBUILD-24758162