RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux bos01-arm64-005 4.2.0-34-generic #39-Ubuntu SMP Thu Mar 10 22:12:07 UTC 2016 aarch64 Buildd toolchain package versions: launchpad-buildd_138 python-lpbuildd_138 sbuild_0.65.2-1ubuntu2+ubuntu15.10.3 bzr-builder_0.7.3-0ubuntu1 bzr_2.6.0+bzr6602-2ubuntu4 git-build-recipe_0.3~git201603101733.90b6821~ubuntu15.10.1 git_1:2.5.0-1ubuntu0.2 dpkg-dev_1.18.2ubuntu5.1 python-debian_0.1.27ubuntu1 qemu-user-static_1:2.3+dfsg-5ubuntu9.2. Syncing the system clock with the buildd NTP service... 19 May 23:13:12 ntpdate[8343]: adjust time server 10.211.37.1 offset -0.000192 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-9774390', '/home/buildd/filecache-default/69d3533015def2fc9828d1a0131b60ffb6ebf960'] Unpacking chroot for build PACKAGEBUILD-9774390 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-9774390'] Mounting chroot for build PACKAGEBUILD-9774390 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-9774390', 'deb http://ftpmaster.internal/ubuntu yakkety main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-security main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-updates main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-9774390 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-9774390', 'arm64'] Updating debian chroot for build PACKAGEBUILD-9774390 Get:1 http://ftpmaster.internal/ubuntu yakkety InRelease [247 kB] Get:2 http://ftpmaster.internal/ubuntu yakkety-security InRelease [92.2 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety-updates InRelease [92.2 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety-proposed InRelease [95.7 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main arm64 Packages [1132 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main Translation-en [567 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/universe arm64 Packages [7471 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/universe Translation-en [4433 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety-security/main arm64 Packages [64 B] Get:10 http://ftpmaster.internal/ubuntu yakkety-security/main Translation-en [64 B] Get:11 http://ftpmaster.internal/ubuntu yakkety-security/universe arm64 Packages [64 B] Get:12 http://ftpmaster.internal/ubuntu yakkety-security/universe Translation-en [64 B] Get:13 http://ftpmaster.internal/ubuntu yakkety-updates/main arm64 Packages [64 B] Get:14 http://ftpmaster.internal/ubuntu yakkety-updates/main Translation-en [64 B] Get:15 http://ftpmaster.internal/ubuntu yakkety-updates/universe arm64 Packages [64 B] Get:16 http://ftpmaster.internal/ubuntu yakkety-updates/universe Translation-en [64 B] Get:17 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 Packages [76.6 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety-proposed/main Translation-en [39.8 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety-proposed/universe arm64 Packages [216 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety-proposed/universe Translation-en [117 kB] Fetched 14.6 MB in 5s (2875 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libpng16-16 The following packages will be upgraded: apt apt-transport-https bash binutils bzip2 cpp-5 debconf dmsetup dpkg dpkg-dev g++-5 gcc-5 gcc-5-base gcc-6-base grep hostname init init-system-helpers initscripts libapt-pkg5.0 libasan2 libasn1-8-heimdal libatomic1 libbz2-1.0 libcap2 libcap2-bin libcc1-0 libdevmapper1.02.1 libdpkg-perl libgcc-5-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libitm1 libkrb5-26-heimdal libldap-2.4-2 libperl5.22 libpng12-0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libusb-0.1-4 libwind0-heimdal linux-libc-dev lsb-base make optipng perl perl-base perl-modules-5.22 policyrcd-script-zg2 sed systemd systemd-sysv sysv-rc sysvinit-utils tar tzdata ubuntu-keyring zlib1g 79 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 79.2 MB of archives. After this operation, 205 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu yakkety/main arm64 bash arm64 4.3-14ubuntu2 [518 kB] Get:2 http://ftpmaster.internal/ubuntu yakkety/main arm64 dpkg arm64 1.18.7ubuntu1 [2091 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety/main arm64 grep arm64 2.25-1 [137 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety/main arm64 hostname arm64 3.17ubuntu1 [11.3 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main arm64 perl-modules-5.22 all 5.22.2-1 [2642 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main arm64 libperl5.22 arm64 5.22.2-1 [2797 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/main arm64 perl arm64 5.22.2-1 [237 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/main arm64 perl-base arm64 5.22.2-1 [1141 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety/main arm64 bzip2 arm64 1.0.6-8build1 [31.1 kB] Get:10 http://ftpmaster.internal/ubuntu yakkety/main arm64 libbz2-1.0 arm64 1.0.6-8build1 [28.6 kB] Get:11 http://ftpmaster.internal/ubuntu yakkety/main arm64 zlib1g arm64 1:1.2.8.dfsg-2ubuntu5 [45.5 kB] Get:12 http://ftpmaster.internal/ubuntu yakkety/main arm64 init-system-helpers all 1.33ubuntu1 [31.9 kB] Get:13 http://ftpmaster.internal/ubuntu yakkety/main arm64 init arm64 1.33ubuntu1 [4382 B] Get:14 http://ftpmaster.internal/ubuntu yakkety/main arm64 sed arm64 4.2.2-7.1 [134 kB] Get:15 http://ftpmaster.internal/ubuntu yakkety/main arm64 tar arm64 1.29-1 [187 kB] Get:16 http://ftpmaster.internal/ubuntu yakkety/main arm64 gcc-6-base arm64 6.1.1-3ubuntu11 [16.9 kB] Get:17 http://ftpmaster.internal/ubuntu yakkety/main arm64 libgcc1 arm64 1:6.1.1-3ubuntu11 [30.2 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety/main arm64 libstdc++6 arm64 6.1.1-3ubuntu11 [368 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety/main arm64 libapt-pkg5.0 arm64 1.3~exp1 [652 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety/main arm64 ubuntu-keyring all 2016.05.13 [16.5 kB] Get:21 http://ftpmaster.internal/ubuntu yakkety/main arm64 apt arm64 1.3~exp1 [1010 kB] Get:22 http://ftpmaster.internal/ubuntu yakkety/main arm64 debconf all 1.5.59ubuntu1 [136 kB] Get:23 http://ftpmaster.internal/ubuntu yakkety/main arm64 libgpg-error0 arm64 1.22-2 [29.7 kB] Get:24 http://ftpmaster.internal/ubuntu yakkety/main arm64 libgcrypt20 arm64 1.7.0-2 [301 kB] Get:25 http://ftpmaster.internal/ubuntu yakkety/main arm64 sysvinit-utils arm64 2.88dsf-59.3ubuntu5 [20.9 kB] Get:26 http://ftpmaster.internal/ubuntu yakkety/main arm64 sysv-rc all 2.88dsf-59.3ubuntu5 [18.2 kB] Get:27 http://ftpmaster.internal/ubuntu yakkety/main arm64 libsystemd0 arm64 229-6ubuntu1 [172 kB] Get:28 http://ftpmaster.internal/ubuntu yakkety/main arm64 initscripts arm64 2.88dsf-59.3ubuntu5 [24.7 kB] Get:29 http://ftpmaster.internal/ubuntu yakkety/main arm64 systemd arm64 229-6ubuntu1 [2971 kB] Get:30 http://ftpmaster.internal/ubuntu yakkety/main arm64 lsb-base all 9.20160110ubuntu1 [13.7 kB] Get:31 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libcap2 arm64 1:2.25-1 [12.6 kB] Get:32 http://ftpmaster.internal/ubuntu yakkety/main arm64 libselinux1 arm64 2.5-3 [53.9 kB] Get:33 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libcap2-bin arm64 1:2.25-1 [19.9 kB] Get:34 http://ftpmaster.internal/ubuntu yakkety/main arm64 systemd-sysv arm64 229-6ubuntu1 [17.6 kB] Get:35 http://ftpmaster.internal/ubuntu yakkety/main arm64 libudev1 arm64 229-6ubuntu1 [51.0 kB] Get:36 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libdevmapper1.02.1 arm64 2:1.02.124-1ubuntu1 [116 kB] Get:37 http://ftpmaster.internal/ubuntu yakkety/main arm64 libsepol1 arm64 2.5-1 [175 kB] Get:38 http://ftpmaster.internal/ubuntu yakkety/main arm64 libsemanage-common all 2.5-1 [6800 B] Get:39 http://ftpmaster.internal/ubuntu yakkety/main arm64 libsemanage1 arm64 2.5-1 [65.9 kB] Get:40 http://ftpmaster.internal/ubuntu yakkety/main arm64 libusb-0.1-4 arm64 2:0.1.12-30 [15.1 kB] Get:41 http://ftpmaster.internal/ubuntu yakkety/main arm64 tzdata all 2016d-2 [168 kB] Get:42 http://ftpmaster.internal/ubuntu yakkety/main arm64 libtasn1-6 arm64 4.8-1 [37.2 kB] Get:43 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libgnutls30 arm64 3.4.11-4ubuntu1 [440 kB] Get:44 http://ftpmaster.internal/ubuntu yakkety/main arm64 libslang2 arm64 2.3.0-2.3ubuntu1 [357 kB] Get:45 http://ftpmaster.internal/ubuntu yakkety/main arm64 apt-transport-https arm64 1.3~exp1 [24.3 kB] Get:46 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libroken18-heimdal arm64 1.7~git20160515+dfsg-1 [34.6 kB] Get:47 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libasn1-8-heimdal arm64 1.7~git20160515+dfsg-1 [127 kB] Get:48 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libheimbase1-heimdal arm64 1.7~git20160515+dfsg-1 [24.4 kB] Get:49 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libhcrypto4-heimdal arm64 1.7~git20160515+dfsg-1 [74.0 kB] Get:50 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libwind0-heimdal arm64 1.7~git20160515+dfsg-1 [47.1 kB] Get:51 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libhx509-5-heimdal arm64 1.7~git20160515+dfsg-1 [86.5 kB] Get:52 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libkrb5-26-heimdal arm64 1.7~git20160515+dfsg-1 [162 kB] Get:53 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libheimntlm0-heimdal arm64 1.7~git20160515+dfsg-1 [13.1 kB] Get:54 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 libgssapi3-heimdal arm64 1.7~git20160515+dfsg-1 [77.1 kB] Get:55 http://ftpmaster.internal/ubuntu yakkety/main arm64 libsasl2-modules-db arm64 2.1.26.dfsg1-15 [12.9 kB] Get:56 http://ftpmaster.internal/ubuntu yakkety/main arm64 libsasl2-2 arm64 2.1.26.dfsg1-15 [41.5 kB] Get:57 http://ftpmaster.internal/ubuntu yakkety/main arm64 libldap-2.4-2 arm64 2.4.42+dfsg-2ubuntu4 [135 kB] Get:58 http://ftpmaster.internal/ubuntu yakkety/main arm64 libpng16-16 arm64 1.6.21-5 [159 kB] Get:59 http://ftpmaster.internal/ubuntu yakkety/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-1 [48.2 kB] Get:60 http://ftpmaster.internal/ubuntu yakkety/main arm64 binutils arm64 2.26-9ubuntu1 [2457 kB] Get:61 http://ftpmaster.internal/ubuntu yakkety/main arm64 libgomp1 arm64 6.1.1-3ubuntu11 [61.8 kB] Get:62 http://ftpmaster.internal/ubuntu yakkety/main arm64 libitm1 arm64 6.1.1-3ubuntu11 [24.9 kB] Get:63 http://ftpmaster.internal/ubuntu yakkety/main arm64 libatomic1 arm64 6.1.1-3ubuntu11 [6586 B] Get:64 http://ftpmaster.internal/ubuntu yakkety/main arm64 libasan2 arm64 5.3.1-19ubuntu1 [232 kB] Get:65 http://ftpmaster.internal/ubuntu yakkety/main arm64 libubsan0 arm64 6.1.1-3ubuntu11 [96.9 kB] Get:66 http://ftpmaster.internal/ubuntu yakkety/main arm64 g++-5 arm64 5.3.1-19ubuntu1 [25.0 MB] Get:67 http://ftpmaster.internal/ubuntu yakkety/main arm64 gcc-5 arm64 5.3.1-19ubuntu1 [5536 kB] Get:68 http://ftpmaster.internal/ubuntu yakkety/main arm64 libstdc++-5-dev arm64 5.3.1-19ubuntu1 [1354 kB] Get:69 http://ftpmaster.internal/ubuntu yakkety/main arm64 libgcc-5-dev arm64 5.3.1-19ubuntu1 [487 kB] Get:70 http://ftpmaster.internal/ubuntu yakkety/main arm64 libcc1-0 arm64 6.1.1-3ubuntu11 [27.3 kB] Get:71 http://ftpmaster.internal/ubuntu yakkety/main arm64 cpp-5 arm64 5.3.1-19ubuntu1 [23.4 MB] Get:72 http://ftpmaster.internal/ubuntu yakkety/main arm64 gcc-5-base arm64 5.3.1-19ubuntu1 [17.3 kB] Get:73 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 dmsetup arm64 2:1.02.124-1ubuntu1 [63.4 kB] Get:74 http://ftpmaster.internal/ubuntu yakkety/main arm64 dpkg-dev all 1.18.7ubuntu1 [666 kB] Get:75 http://ftpmaster.internal/ubuntu yakkety/main arm64 libdpkg-perl all 1.18.7ubuntu1 [202 kB] Get:76 http://ftpmaster.internal/ubuntu yakkety/main arm64 make arm64 4.1-9 [137 kB] Get:77 http://ftpmaster.internal/ubuntu yakkety/universe arm64 libpng12-0 arm64 1.2.54-6ubuntu1 [105 kB] Get:78 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 linux-libc-dev arm64 4.4.0-23.41 [813 kB] Get:79 http://ftpmaster.internal/ubuntu yakkety/main arm64 optipng arm64 0.7.6-1build1 [77.1 kB] Get:80 http://ftpmaster.internal/ubuntu yakkety/main arm64 policyrcd-script-zg2 all 0.1-3 [5610 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 79.2 MB in 7s (10.1 MB/s) (Reading database ... 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Setting up ubuntu-keyring (2016.05.13) ... gpg: key 437D05B5: "Ubuntu Archive Automatic Signing Key " not changed gpg: key FBB75451: "Ubuntu CD Image Automatic Signing Key " not changed gpg: key C0B21F32: "Ubuntu Archive Automatic Signing Key (2012) " not changed gpg: key EFE21092: "Ubuntu CD Image Automatic Signing Key (2012) " not changed gpg: Total number processed: 4 gpg: unchanged: 4 (Reading database ... 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Universal Time is now: Thu May 19 23:14:14 UTC 2016. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libtasn1-6:arm64 (4.8-1) ... Setting up libgnutls30:arm64 (3.4.11-4ubuntu1) ... Setting up libslang2:arm64 (2.3.0-2.3ubuntu1) ... Setting up apt-transport-https (1.3~exp1) ... Setting up libroken18-heimdal:arm64 (1.7~git20160515+dfsg-1) ... Setting up libasn1-8-heimdal:arm64 (1.7~git20160515+dfsg-1) ... Setting up libheimbase1-heimdal:arm64 (1.7~git20160515+dfsg-1) ... Setting up libhcrypto4-heimdal:arm64 (1.7~git20160515+dfsg-1) ... Setting up libwind0-heimdal:arm64 (1.7~git20160515+dfsg-1) ... Setting up libhx509-5-heimdal:arm64 (1.7~git20160515+dfsg-1) ... Setting up libkrb5-26-heimdal:arm64 (1.7~git20160515+dfsg-1) ... Setting up libheimntlm0-heimdal:arm64 (1.7~git20160515+dfsg-1) ... Setting up libgssapi3-heimdal:arm64 (1.7~git20160515+dfsg-1) ... Setting up libsasl2-modules-db:arm64 (2.1.26.dfsg1-15) ... Setting up libsasl2-2:arm64 (2.1.26.dfsg1-15) ... Setting up libldap-2.4-2:arm64 (2.4.42+dfsg-2ubuntu4) ... Setting up libpng16-16:arm64 (1.6.21-5) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-1) ... Setting up binutils (2.26-9ubuntu1) ... Setting up libgomp1:arm64 (6.1.1-3ubuntu11) ... Setting up libitm1:arm64 (6.1.1-3ubuntu11) ... Setting up libatomic1:arm64 (6.1.1-3ubuntu11) ... Setting up gcc-5-base:arm64 (5.3.1-19ubuntu1) ... Setting up libasan2:arm64 (5.3.1-19ubuntu1) ... Setting up libubsan0:arm64 (6.1.1-3ubuntu11) ... Setting up cpp-5 (5.3.1-19ubuntu1) ... Setting up libcc1-0:arm64 (6.1.1-3ubuntu11) ... Setting up libgcc-5-dev:arm64 (5.3.1-19ubuntu1) ... Setting up gcc-5 (5.3.1-19ubuntu1) ... Setting up libstdc++-5-dev:arm64 (5.3.1-19ubuntu1) ... Setting up g++-5 (5.3.1-19ubuntu1) ... Setting up dmsetup (2:1.02.124-1ubuntu1) ... Setting up libdpkg-perl (1.18.7ubuntu1) ... Setting up make (4.1-9) ... Setting up dpkg-dev (1.18.7ubuntu1) ... Setting up libpng12-0:arm64 (1.2.54-6ubuntu1) ... Setting up linux-libc-dev:arm64 (4.4.0-23.41) ... Setting up optipng (0.7.6-1build1) ... Setting up policyrcd-script-zg2 (0.1-3) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Processing triggers for systemd (229-6ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-9774390', 'arm64', 'yakkety-proposed', '-c', 'chroot:autobuild', '--arch=arm64', '--dist=yakkety-proposed', '--purge=never', '--nolog', 'rna-star_2.5.2a+dfsg-1.dsc'] Initiating build PACKAGEBUILD-9774390 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.2.0-34-generic #39-Ubuntu SMP Thu Mar 10 22:12:07 UTC 2016 aarch64 sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bos01-arm64-005.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ rna-star 2.5.2a+dfsg-1 (arm64) 19 May 2016 23:14 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: rna-star Version: 2.5.2a+dfsg-1 Source Version: 2.5.2a+dfsg-1 Distribution: yakkety-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/rna-star-8IypAh/rna-star-2.5.2a+dfsg' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/rna-star-8IypAh' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-9774390/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── rna-star_2.5.2a+dfsg-1.dsc exists in .; copying to chroot Check architectures ─────────────────── Check dependencies ────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-qVkuAu/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/«BUILDDIR»/resolver-qVkuAu/apt_archive ./ InRelease Get:2 copy:/«BUILDDIR»/resolver-qVkuAu/apt_archive ./ Release [2119 B] Ign:3 copy:/«BUILDDIR»/resolver-qVkuAu/apt_archive ./ Release.gpg Get:4 copy:/«BUILDDIR»/resolver-qVkuAu/apt_archive ./ Sources [208 B] Get:5 copy:/«BUILDDIR»/resolver-qVkuAu/apt_archive ./ Packages [524 B] Fetched 2851 B in 0s (132 kB/s) Reading package lists... W: The repository 'copy:/«BUILDDIR»/resolver-qVkuAu/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 770 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Get:1 copy:/«BUILDDIR»/resolver-qVkuAu/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 770 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12081 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), libhts-dev, vim-common, zlib1g-dev Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), libhts-dev, vim-common, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-rna-star-dummy' in '/«BUILDDIR»/resolver-n1ShvH/apt_archive/sbuild-build-depends-rna-star-dummy.deb'. Ign:1 copy:/«BUILDDIR»/resolver-n1ShvH/apt_archive ./ InRelease Get:2 copy:/«BUILDDIR»/resolver-n1ShvH/apt_archive ./ Release [2119 B] Ign:3 copy:/«BUILDDIR»/resolver-n1ShvH/apt_archive ./ Release.gpg Get:4 copy:/«BUILDDIR»/resolver-n1ShvH/apt_archive ./ Sources [440 B] Get:5 copy:/«BUILDDIR»/resolver-n1ShvH/apt_archive ./ Packages [703 B] Fetched 3262 B in 0s (154 kB/s) Reading package lists... W: The repository 'copy:/«BUILDDIR»/resolver-n1ShvH/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install rna-star build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1 libicu57 libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf vim-common zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc groff libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser libmail-box-perl vim-gnome-py2 | vim-gtk-py2 | vim-gtk3-py2 | vim-athena-py2 | vim-nox-py2 Recommended packages: curl | wget | lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl vim | vim-gnome | vim-gtk | vim-gtk3 | vim-athena | vim-nox | vim-tiny The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1 libicu57 libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf sbuild-build-depends-rna-star-dummy vim-common zlib1g-dev 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 16.3 MB of archives. After this operation, 63.7 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-rna-star-dummy Authentication warning overridden. Get:1 copy:/«BUILDDIR»/resolver-n1ShvH/apt_archive ./ sbuild-build-depends-rna-star-dummy 0.invalid.0 [950 B] Get:2 http://ftpmaster.internal/ubuntu yakkety/main arm64 groff-base arm64 1.22.3-7 [1122 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety/main arm64 bsdmainutils arm64 9.0.6ubuntu3 [170 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety/main arm64 libpipeline1 arm64 1.4.1-2 [21.9 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main arm64 man-db arm64 2.7.5-1 [832 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main arm64 libunistring0 arm64 0.9.3-5.2ubuntu1 [251 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/main arm64 libmagic1 arm64 1:5.25-2ubuntu1 [209 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/main arm64 file arm64 1:5.25-2ubuntu1 [21.2 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety/main arm64 vim-common arm64 2:7.4.1689-3ubuntu2 [103 kB] Get:10 http://ftpmaster.internal/ubuntu yakkety/main arm64 libasprintf0v5 arm64 0.19.7-2ubuntu3 [6420 B] Get:11 http://ftpmaster.internal/ubuntu yakkety/main arm64 gettext-base arm64 0.19.7-2ubuntu3 [45.0 kB] Get:12 http://ftpmaster.internal/ubuntu yakkety/main arm64 libglib2.0-0 arm64 2.48.1-1 [926 kB] Get:13 http://ftpmaster.internal/ubuntu yakkety/main arm64 libicu57 arm64 57.1-1 [7529 kB] Get:14 http://ftpmaster.internal/ubuntu yakkety/main arm64 libxml2 arm64 2.9.3+dfsg1-1build1 [565 kB] Get:15 http://ftpmaster.internal/ubuntu yakkety/main arm64 libsigsegv2 arm64 2.10-5 [13.3 kB] Get:16 http://ftpmaster.internal/ubuntu yakkety/main arm64 m4 arm64 1.4.17-5 [184 kB] Get:17 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 autoconf all 2.69-10 [321 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety-proposed/main arm64 autotools-dev all 20160430.1 [39.6 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety/main arm64 automake all 1:1.15-4ubuntu1 [510 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety/main arm64 autopoint all 0.19.7-2ubuntu3 [406 kB] Get:21 http://ftpmaster.internal/ubuntu yakkety/main arm64 libcroco3 arm64 0.6.11-1 [66.0 kB] Get:22 http://ftpmaster.internal/ubuntu yakkety/main arm64 gettext arm64 0.19.7-2ubuntu3 [1015 kB] Get:23 http://ftpmaster.internal/ubuntu yakkety/main arm64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:24 http://ftpmaster.internal/ubuntu yakkety/main arm64 po-debconf all 1.0.19 [234 kB] Get:25 http://ftpmaster.internal/ubuntu yakkety/main arm64 libarchive-zip-perl all 1.57-1 [84.0 kB] Get:26 http://ftpmaster.internal/ubuntu yakkety/main arm64 libfile-stripnondeterminism-perl all 0.016-1 [11.0 kB] Get:27 http://ftpmaster.internal/ubuntu yakkety/main arm64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:28 http://ftpmaster.internal/ubuntu yakkety/main arm64 dh-strip-nondeterminism all 0.016-1 [4858 B] Get:29 http://ftpmaster.internal/ubuntu yakkety/main arm64 libtool all 2.4.6-0.1 [193 kB] Get:30 http://ftpmaster.internal/ubuntu yakkety/main arm64 dh-autoreconf all 12 [15.8 kB] Get:31 http://ftpmaster.internal/ubuntu yakkety/main arm64 debhelper all 9.20160403ubuntu1 [711 kB] Get:32 http://ftpmaster.internal/ubuntu yakkety/universe arm64 libhts1 arm64 1.3.1-1ubuntu1 [211 kB] Get:33 http://ftpmaster.internal/ubuntu yakkety/universe arm64 libhts-dev arm64 1.3.1-1ubuntu1 [279 kB] Get:34 http://ftpmaster.internal/ubuntu yakkety/main arm64 zlib1g-dev arm64 1:1.2.8.dfsg-2ubuntu5 [162 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.3 MB in 2s (7839 kB/s) Selecting previously unselected package groff-base. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12081 files and directories currently installed.) Preparing to unpack .../groff-base_1.22.3-7_arm64.deb ... Unpacking groff-base (1.22.3-7) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6ubuntu3_arm64.deb ... Unpacking bsdmainutils (9.0.6ubuntu3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../libpipeline1_1.4.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.5-1_arm64.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package libunistring0:arm64. Preparing to unpack .../libunistring0_0.9.3-5.2ubuntu1_arm64.deb ... Unpacking libunistring0:arm64 (0.9.3-5.2ubuntu1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../libmagic1_1%3a5.25-2ubuntu1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.25-2ubuntu1) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.25-2ubuntu1_arm64.deb ... Unpacking file (1:5.25-2ubuntu1) ... Selecting previously unselected package vim-common. Preparing to unpack .../vim-common_2%3a7.4.1689-3ubuntu2_arm64.deb ... Unpacking vim-common (2:7.4.1689-3ubuntu2) ... Selecting previously unselected package libasprintf0v5:arm64. Preparing to unpack .../libasprintf0v5_0.19.7-2ubuntu3_arm64.deb ... Unpacking libasprintf0v5:arm64 (0.19.7-2ubuntu3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.19.7-2ubuntu3_arm64.deb ... Unpacking gettext-base (0.19.7-2ubuntu3) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../libglib2.0-0_2.48.1-1_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.48.1-1) ... Selecting previously unselected package libicu57:arm64. Preparing to unpack .../libicu57_57.1-1_arm64.deb ... Unpacking libicu57:arm64 (57.1-1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../libxml2_2.9.3+dfsg1-1build1_arm64.deb ... Unpacking libxml2:arm64 (2.9.3+dfsg1-1build1) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../libsigsegv2_2.10-5_arm64.deb ... Unpacking libsigsegv2:arm64 (2.10-5) ... Selecting previously unselected package m4. Preparing to unpack .../archives/m4_1.4.17-5_arm64.deb ... Unpacking m4 (1.4.17-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../autoconf_2.69-10_all.deb ... Unpacking autoconf (2.69-10) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../autotools-dev_20160430.1_all.deb ... Unpacking autotools-dev (20160430.1) ... Selecting previously unselected package automake. Preparing to unpack .../automake_1%3a1.15-4ubuntu1_all.deb ... Unpacking automake (1:1.15-4ubuntu1) ... Selecting previously unselected package autopoint. Preparing to unpack .../autopoint_0.19.7-2ubuntu3_all.deb ... Unpacking autopoint (0.19.7-2ubuntu3) ... Selecting previously unselected package libcroco3:arm64. Preparing to unpack .../libcroco3_0.6.11-1_arm64.deb ... Unpacking libcroco3:arm64 (0.6.11-1) ... Selecting previously unselected package gettext. Preparing to unpack .../gettext_0.19.7-2ubuntu3_arm64.deb ... Unpacking gettext (0.19.7-2ubuntu3) ... Selecting previously unselected package intltool-debian. 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Selecting previously unselected package sbuild-build-depends-rna-star-dummy. Preparing to unpack .../sbuild-build-depends-rna-star-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-rna-star-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... 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:arm64 (1.4.1-2) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libunistring0:arm64 (0.9.3-5.2ubuntu1) ... Setting up libmagic1:arm64 (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up vim-common (2:7.4.1689-3ubuntu2) ... Setting up libasprintf0v5:arm64 (0.19.7-2ubuntu3) ... Setting up gettext-base (0.19.7-2ubuntu3) ... Setting up libglib2.0-0:arm64 (2.48.1-1) ... No schema files found: doing nothing. Setting up libicu57:arm64 (57.1-1) ... Setting up libxml2:arm64 (2.9.3+dfsg1-1build1) ... Setting up libsigsegv2:arm64 (2.10-5) ... Setting up m4 (1.4.17-5) ... Setting up autoconf (2.69-10) ... Setting up autotools-dev (20160430.1) ... Setting up automake (1:1.15-4ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up autopoint (0.19.7-2ubuntu3) ... Setting up libcroco3:arm64 (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 (1.57-1) ... Setting up libfile-stripnondeterminism-perl (0.016-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libtool (2.4.6-0.1) ... Setting up libhts1:arm64 (1.3.1-1ubuntu1) ... Setting up libhts-dev:arm64 (1.3.1-1ubuntu1) ... Setting up zlib1g-dev:arm64 (1:1.2.8.dfsg-2ubuntu5) ... Setting up dh-autoreconf (12) ... Setting up debhelper (9.20160403ubuntu1) ... Setting up sbuild-build-depends-rna-star-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.016-1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 4.2.0-34-generic arm64 (aarch64) Toolchain package versions: binutils_2.26-9ubuntu1 dpkg-dev_1.18.7ubuntu1 g++-5_5.3.1-19ubuntu1 gcc-5_5.3.1-19ubuntu1 libc6-dev_2.23-0ubuntu3 libstdc++-5-dev_5.3.1-19ubuntu1 libstdc++6_6.1.1-3ubuntu11 linux-libc-dev_4.4.0-23.41 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.3~exp1 apt-transport-https_1.3~exp1 autoconf_2.69-10 automake_1:1.15-4ubuntu1 autopoint_0.19.7-2ubuntu3 autotools-dev_20160430.1 base-files_9.6ubuntu1 base-passwd_3.5.39 bash_4.3-14ubuntu2 binutils_2.26-9ubuntu1 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.27.1-6ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8build1 ca-certificates_20160104ubuntu1 coreutils_8.25-2ubuntu2 cpp_4:5.3.1-1ubuntu1 cpp-5_5.3.1-19ubuntu1 dash_0.5.8-2.1ubuntu2 debconf_1.5.59ubuntu1 debhelper_9.20160403ubuntu1 debianutils_4.7 dh-autoreconf_12 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.124-1ubuntu1 dpkg_1.18.7ubuntu1 dpkg-dev_1.18.7ubuntu1 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_5.3.1-19ubuntu1 gcc_4:5.3.1-1ubuntu1 gcc-5_5.3.1-19ubuntu1 gcc-5-base_5.3.1-19ubuntu1 gcc-6-base_6.1.1-3ubuntu11 gettext_0.19.7-2ubuntu3 gettext-base_0.19.7-2ubuntu3 gnupg_1.4.20-1ubuntu3 gpgv_1.4.20-1ubuntu3 grep_2.25-1 groff-base_1.22.3-7 gzip_1.6-4ubuntu1 hostname_3.17ubuntu1 init_1.33ubuntu1 init-system-helpers_1.33ubuntu1 initscripts_2.88dsf-59.3ubuntu5 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapparmor1_2.10.95-0ubuntu2 libapt-pkg5.0_1.3~exp1 libarchive-zip-perl_1.57-1 libasan2_5.3.1-19ubuntu1 libasn1-8-heimdal_1.7~git20160515+dfsg-1 libasprintf0v5_0.19.7-2ubuntu3 libatomic1_6.1.1-3ubuntu11 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1ubuntu2 libaudit1_1:2.4.5-1ubuntu2 libblkid1_2.27.1-6ubuntu3 libbz2-1.0_1.0.6-8build1 libc-bin_2.23-0ubuntu3 libc-dev-bin_2.23-0ubuntu3 libc6_2.23-0ubuntu3 libc6-dev_2.23-0ubuntu3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-3ubuntu11 libcomerr2_1.42.13-1ubuntu1 libcroco3_0.6.11-1 libcryptsetup4_2:1.6.6-5ubuntu2 libcurl3-gnutls_7.47.0-1ubuntu2 libdb5.3_5.3.28-11 libdebconfclient0_0.198ubuntu1 libdevmapper1.02.1_2:1.02.124-1ubuntu1 libdpkg-perl_1.18.7ubuntu1 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.27.1-6ubuntu3 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgcc-5-dev_5.3.1-19ubuntu1 libgcc1_1:6.1.1-3ubuntu11 libgcrypt20_1.7.0-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.48.1-1 libgmp10_2:6.1.0+dfsg-2 libgnutls30_3.4.11-4ubuntu1 libgomp1_6.1.1-3ubuntu11 libgpg-error0_1.22-2 libgssapi-krb5-2_1.13.2+dfsg-5 libgssapi3-heimdal_1.7~git20160515+dfsg-1 libhcrypto4-heimdal_1.7~git20160515+dfsg-1 libheimbase1-heimdal_1.7~git20160515+dfsg-1 libheimntlm0-heimdal_1.7~git20160515+dfsg-1 libhogweed4_3.2-1 libhts-dev_1.3.1-1ubuntu1 libhts1_1.3.1-1ubuntu1 libhx509-5-heimdal_1.7~git20160515+dfsg-1 libicu57_57.1-1 libidn11_1.32-3ubuntu1 libisl15_0.16.1-1 libitm1_6.1.1-3ubuntu11 libk5crypto3_1.13.2+dfsg-5 libkeyutils1_1.5.9-8ubuntu1 libkmod2_22-1ubuntu4 libkrb5-26-heimdal_1.7~git20160515+dfsg-1 libkrb5-3_1.13.2+dfsg-5 libkrb5support0_1.13.2+dfsg-5 libldap-2.4-2_2.4.42+dfsg-2ubuntu4 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.25-2ubuntu1 libmount1_2.27.1-6ubuntu3 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160213-1ubuntu1 libncursesw5_6.0+20160213-1ubuntu1 libnettle6_3.2-1 libp11-kit0_0.23.2-3 libpam-modules_1.1.8-3.2ubuntu2 libpam-modules-bin_1.1.8-3.2ubuntu2 libpam-runtime_1.1.8-3.2ubuntu2 libpam0g_1.1.8-3.2ubuntu2 libpcre3_2:8.38-3.1 libperl5.22_5.22.2-1 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6ubuntu1 libpng16-16_1.6.21-5 libprocps4_2:3.3.10-4ubuntu2 libreadline6_6.3-8ubuntu2 libroken18-heimdal_1.7~git20160515+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.2.3-3ubuntu3 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libslang2_2.3.0-2.3ubuntu1 libsmartcols1_2.27.1-6ubuntu3 libsqlite3-0_3.11.0-1ubuntu1 libss2_1.42.13-1ubuntu1 libssl1.0.0_1.0.2g-1ubuntu4 libstdc++-5-dev_5.3.1-19ubuntu1 libstdc++6_6.1.1-3ubuntu11 libsystemd0_229-6ubuntu1 libtasn1-6_4.8-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160213-1ubuntu1 libtool_2.4.6-0.1 libubsan0_6.1.1-3ubuntu11 libudev1_229-6ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6ubuntu3 libwind0-heimdal_1.7~git20160515+dfsg-1 libxml2_2.9.3+dfsg1-1build1 linux-libc-dev_4.4.0-23.41 lockfile-progs_0.1.17 login_1:4.2-3.1ubuntu5 lsb-base_9.20160110ubuntu1 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mount_2.27.1-6ubuntu3 multiarch-support_2.23-0ubuntu3 ncurses-base_6.0+20160213-1ubuntu1 ncurses-bin_6.0+20160213-1ubuntu1 openssl_1.0.2g-1ubuntu4 optipng_0.7.6-1build1 passwd_1:4.2-3.1ubuntu5 patch_2.7.5-1 perl_5.22.2-1 perl-base_5.22.2-1 perl-modules-5.22_5.22.2-1 pkg-create-dbgsym_0.72 pkgbinarymangler_129 po-debconf_1.0.19 policyrcd-script-zg2_0.1-3 procps_2:3.3.10-4ubuntu2 readline-common_6.3-8ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-rna-star-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 systemd_229-6ubuntu1 systemd-sysv_229-6ubuntu1 sysv-rc_2.88dsf-59.3ubuntu5 sysvinit-utils_2.88dsf-59.3ubuntu5 tar_1.29-1 tzdata_2016d-2 ubuntu-keyring_2016.05.13 util-linux_2.27.1-6ubuntu3 vim-common_2:7.4.1689-3ubuntu2 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu5 zlib1g-dev_1:1.2.8.dfsg-2ubuntu5 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Thu May 19 16:15:02 2016 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./rna-star_2.5.2a+dfsg-1.dsc dpkg-source: info: extracting rna-star in rna-star-2.5.2a+dfsg dpkg-source: info: unpacking rna-star_2.5.2a+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.5.2a+dfsg-1.debian.tar.xz dpkg-source: info: applying donotuse_own_htslib.patch dpkg-source: info: applying mips_shm_noreserve.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/«BUILDDIR»/rna-star-2.5.2a+dfsg SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«BUILDDIR»/rna-star-2.5.2a+dfsg' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ───────────────── dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.5.2a+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build rna-star-2.5.2a+dfsg dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory '/«BUILDDIR»/rna-star-2.5.2a+dfsg' cd source && /usr/bin/make clean make[2]: Entering directory '/«BUILDDIR»/rna-star-2.5.2a+dfsg/source' rm -f *.o STAR STARstatic STARlong Depend.list make[2]: Leaving directory '/«BUILDDIR»/rna-star-2.5.2a+dfsg/source' rm -f source/parametersDefault.xxd make[1]: Leaving directory '/«BUILDDIR»/rna-star-2.5.2a+dfsg' dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_update_autotools_config -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/«BUILDDIR»/rna-star-2.5.2a+dfsg' cd source && /usr/bin/make CCFLAGS_common_add="-flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/«BUILDDIR»/rna-star-2.5.2a+dfsg/source' Makefile:89: Depend.list: No such file or directory xxd -i parametersDefault > parametersDefault.xxd echo sjdbLoadFromFiles.cpp blocksOverlap.cpp sjdbPrepare.cpp genomeScanFastaFiles.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp ReadAlign_createExtendWindowsWithAlign.cpp readLoad.cpp binarySearch2.cpp sjdbInsertJunctions.cpp Transcriptome_geneCountsAddAlign.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp STAR.cpp BAMbinSortByCoordinate.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlignChunk.cpp sortSuffixesBucket.cpp ReadAlign_oneRead.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp Parameters_openReadsFiles.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp genomeSAindex.cpp signalFromBAM.cpp sjdbLoadFromStream.cpp genomeGenerate.cpp Parameters_closeReadsFiles.cpp stitchWindowAligns.cpp GlobalVariables.cpp Parameters.cpp sjSplitAlign.cpp Transcriptome.cpp ReadAlign_chimericDetection.cpp outputSJ.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp ThreadControl.cpp Genome_insertSequences.cpp Genome.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp BAMoutput.cpp genomeParametersWrite.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp BAMbinSortUnmapped.cpp SharedMemory.cpp sysRemoveDir.cpp Quantifications.cpp bamRemoveDuplicates.cpp InOutStreams.cpp ReadAlign_storeAligns.cpp stringSubstituteAll.cpp Transcript.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp SequenceFuns.cpp extendAlign.cpp BAMfunctions.cpp OutSJ.cpp bam_cat.c sjdbLoadFromFiles.cpp blocksOverlap.cpp sjdbPrepare.cpp genomeScanFastaFiles.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp ReadAlign_createExtendWindowsWithAlign.cpp readLoad.cpp binarySearch2.cpp sjdbInsertJunctions.cpp Transcriptome_geneCountsAddAlign.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp STAR.cpp BAMbinSortByCoordinate.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlignChunk.cpp sortSuffixesBucket.cpp ReadAlign_oneRead.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp Parameters_openReadsFiles.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp genomeSAindex.cpp signalFromBAM.cpp sjdbLoadFromStream.cpp genomeGenerate.cpp Parameters_closeReadsFiles.cpp stitchWindowAligns.cpp GlobalVariables.cpp Parameters.cpp sjSplitAlign.cpp Transcriptome.cpp ReadAlign_chimericDetection.cpp outputSJ.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp ThreadControl.cpp Genome_insertSequences.cpp Genome.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp BAMoutput.cpp genomeParametersWrite.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp BAMbinSortUnmapped.cpp SharedMemory.cpp sysRemoveDir.cpp Quantifications.cpp bamRemoveDuplicates.cpp InOutStreams.cpp ReadAlign_storeAligns.cpp stringSubstituteAll.cpp Transcript.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp SequenceFuns.cpp extendAlign.cpp BAMfunctions.cpp OutSJ.cpp bam_cat.c /bin/rm -f ./Depend.list g++ -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:40 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM sjdbLoadFromFiles.cpp blocksOverlap.cpp sjdbPrepare.cpp genomeScanFastaFiles.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp ReadAlign_createExtendWindowsWithAlign.cpp readLoad.cpp binarySearch2.cpp sjdbInsertJunctions.cpp Transcriptome_geneCountsAddAlign.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp STAR.cpp BAMbinSortByCoordinate.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlignChunk.cpp sortSuffixesBucket.cpp ReadAlign_oneRead.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp Parameters_openReadsFiles.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp genomeSAindex.cpp signalFromBAM.cpp sjdbLoadFromStream.cpp genomeGenerate.cpp Parameters_closeReadsFiles.cpp stitchWindowAligns.cpp GlobalVariables.cpp Parameters.cpp sjSplitAlign.cpp Transcriptome.cpp ReadAlign_chimericDetection.cpp outputSJ.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp ThreadControl.cpp Genome_insertSequences.cpp Genome.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp BAMoutput.cpp genomeParametersWrite.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp BAMbinSortUnmapped.cpp SharedMemory.cpp sysRemoveDir.cpp Quantifications.cpp bamRemoveDuplicates.cpp InOutStreams.cpp ReadAlign_storeAligns.cpp stringSubstituteAll.cpp Transcript.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp SequenceFuns.cpp extendAlign.cpp BAMfunctions.cpp OutSJ.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:299:49: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(P->inOut->outBAMfileUnsorted); ^ STAR.cpp:303:46: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(P->inOut->outQuantBAMfile); ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' sysRemoveDir.cpp sysRemoveDir.cpp:7:58: warning: unused parameter ‘sb’ [-Wunused-parameter] int removeFileOrDir(const char *fpath,const struct stat *sb, int typeflag, struct FTW *ftwbuf) { ^ sysRemoveDir.cpp:7:88: warning: unused parameter ‘ftwbuf’ [-Wunused-parameter] int removeFileOrDir(const char *fpath,const struct stat *sb, int typeflag, struct FTW *ftwbuf) { ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' alignSmithWaterman.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' sortSuffixesBucket.cpp sortSuffixesBucket.cpp: In function ‘void sortSuffixesBucket(char*, void*, int, int)’: sortSuffixesBucket.cpp:27:43: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] uint64_t iprev=*(uint64_t*)(ind+0*indSkip); ^ sortSuffixesBucket.cpp:31:37: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] if (*(uint64_t*)(ind+id*indSkip)==iprev) ^ sortSuffixesBucket.cpp:43:43: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] iprev=*(uint64_t*)(ind+id*indSkip); ^ sortSuffixesBucket.cpp:62:49: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] charCount[G[*(uint64_t*)(ind+id*indSkip+8) + charShift]]++;//TODO can template uint64_t ^ sortSuffixesBucket.cpp:62:57: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] charCount[G[*(uint64_t*)(ind+id*indSkip+8) + charShift]]++;//TODO can template uint64_t ^ sortSuffixesBucket.cpp:62:72: warning: array subscript has type ‘char’ [-Wchar-subscripts] charCount[G[*(uint64_t*)(ind+id*indSkip+8) + charShift]]++;//TODO can template uint64_t ^ sortSuffixesBucket.cpp:85:50: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] char c=G[*(uint64_t*)(ind+id*indSkip+8) + charShift]; ^ sortSuffixesBucket.cpp:85:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] char c=G[*(uint64_t*)(ind+id*indSkip+8) + charShift]; ^ sortSuffixesBucket.cpp:86:44: warning: array subscript has type ‘char’ [-Wchar-subscripts] memcpy(ind1+charStart[c]*indSkip, ind+id*indSkip, indSkip); ^ sortSuffixesBucket.cpp:86:62: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] memcpy(ind1+charStart[c]*indSkip, ind+id*indSkip, indSkip); ^ sortSuffixesBucket.cpp:87:32: warning: array subscript has type ‘char’ [-Wchar-subscripts] charStart[c]++; ^ sortSuffixesBucket.cpp:89:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] memcpy(ind+uB1[iu]*indSkip, ind1+uB1[iu]*indSkip, (uB2[iu]-uB1[iu])*indSkip); ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' funCompareUintAndSuffixesMemcmp.cpp funCompareUintAndSuffixesMemcmp.cpp: In function ‘int funCompareUintAndSuffixesMemcmp(const void*, const void*)’: funCompareUintAndSuffixesMemcmp.cpp:21:15: warning: unused variable ‘p5’ [-Wunused-variable] char *p5=g_funCompareUintAndSuffixesMemcmp_G+va[1]+g_funCompareUintAndSuffixesMemcmp_L; ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' loadGTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' BAMoutput.cpp BAMoutput.cpp: In member function ‘void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)’: BAMoutput.cpp:62:47: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfBAM,bamArray,binBytes1); ^ BAMoutput.cpp: In member function ‘void BAMoutput::unsortedFlush()’: BAMoutput.cpp:75:43: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfBAM,bamArray,binBytes1); ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' BAMfunctions.cpp BAMfunctions.cpp: In function ‘void outBAMwriteHeader(BGZF*, const string&, const std::vector >&, const std::vector&)’: BAMfunctions.cpp:76:31: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp,"BAM\001",4); ^ BAMfunctions.cpp:78:46: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp,(char*) &hlen,sizeof(hlen)); ^ BAMfunctions.cpp:79:37: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp,samh.c_str(),hlen); ^ BAMfunctions.cpp:81:46: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp,(char*) &nchr,sizeof(nchr)); ^ BAMfunctions.cpp:85:50: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp,(char*) &rlen,sizeof(rlen)); ^ BAMfunctions.cpp:86:47: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string ^ BAMfunctions.cpp:87:50: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp,(char*) &slen,sizeof(slen)); ^ BAMfunctions.cpp:89:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(fp); ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' BAMbinSortByCoordinate.cpp BAMbinSortByCoordinate.cpp: In function ‘void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::__cxx11::string, Parameters*)’: BAMbinSortByCoordinate.cpp:56:64: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfBin,ib, *((uint32*) ib)+sizeof(uint32) ); ^ BAMbinSortByCoordinate.cpp:59:24: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(bgzfBin); ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' bamRemoveDuplicates.cpp bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::__cxx11::string, std::__cxx11::string, Parameters*)’: bamRemoveDuplicates.cpp:125:38: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result] bam_hdr_write(bgzfOut, bamHeader); ^ bamRemoveDuplicates.cpp:152:48: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfOut,bamRaw,bamS); ^ bamRemoveDuplicates.cpp:233:41: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfOut,bamRaw,bamLength); ^ bamRemoveDuplicates.cpp:234:24: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(bgzfOut); ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' BAMbinSortUnmapped.cpp BAMbinSortUnmapped.cpp:5:78: warning: unused parameter ‘bgzfBAM’ [-Wunused-parameter] void BAMbinSortUnmapped(uint32 iBin, uint nThreads, string dirBAMsort, BGZF *bgzfBAM, Parameters *P) { ^ BAMbinSortUnmapped.cpp: In function ‘void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::__cxx11::string, BGZF*, Parameters*)’: BAMbinSortUnmapped.cpp:45:59: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfBin, bamIn[it], bamSize.at(it)); ^ BAMbinSortUnmapped.cpp:62:24: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(bgzfBin); ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -Wall -Wextra -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' bam_cat.c bam_cat.c: In function ‘int bam_cat(int, char* const*, const bam_hdr_t*, const char*)’: bam_cat.c:80:32: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result] if (h) bam_hdr_write(fp, h); ^ bam_cat.c:96:53: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result] if (h == 0 && i == 0) bam_hdr_write(fp, old); ^ bam_cat.c:99:123: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); ^ bam_cat.c:100:27: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(fp); ^ bam_cat.c:111:46: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_raw_write(fp, ebuf, len); ^ bam_cat.c:115:54: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] if(j!=0) bgzf_raw_write(fp, ebuf, es); ^ bam_cat.c:118:45: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_raw_write(fp, buf, len); ^ bam_cat.c:131:45: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_raw_write(fp, ebuf, es); ^ g++ -o STAR -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu May 19 23:14:49 UTC 2016 :/«BUILDDIR»/rna-star-2.5.2a+dfsg/source"' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security SharedMemory.o PackedArray.o SuffixArrayFuns.o STAR.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Stats.o Transcript.o Transcript_alignScore.o ReadAlign.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputAlignments.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_chimericDetection.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o sortSuffixesBucket.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o bam_cat.o GlobalVariables.cpp -pthread -Bstatic -lhts -Bdynamic -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now Parameters_openReadsFiles.cpp: In member function ‘void Parameters::openReadsFiles()’: Parameters_openReadsFiles.cpp:58:97: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(("ls -lL " + file1 + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); ^ Parameters_openReadsFiles.cpp: In member function ‘openReadsFiles’: Parameters_openReadsFiles.cpp:30:20: warning: variable ‘imate’ might be clobbered by ‘longjmp’ or ‘vfork’ [-Wclobbered] for (uint imate=0;imate= 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 dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a 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 arm64: rna-star dh_gencontrol debug symbol wrapper: packages to act on: rna-star dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package rna-star (pkgdir debian/rna-star, ddeb package dir debian/rna-star-dbgsym) dh_gencontrol debug symbol wrapper: building rna-star-dbgsym_2.5.2a+dfsg-1_arm64.ddeb dpkg-deb: building package 'rna-star-dbgsym' in '../rna-star-dbgsym_2.5.2a+dfsg-1_arm64.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile rna-star-dbgsym_2.5.2a+dfsg-1_arm64.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 129 pkgstriptranslations: processing rna-star (in debian/rna-star); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/rna-star/DEBIAN/control, package rna-star, directory debian/rna-star pkgstripfiles: Running PNG optimization (using 4 cpus) for package rna-star ... pkgstripfiles: No PNG files. dpkg-deb: building package 'rna-star' in '../rna-star_2.5.2a+dfsg-1_arm64.deb'. dpkg-genchanges --build=any -mLaunchpad Build Daemon >../rna-star_2.5.2a+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build rna-star-2.5.2a+dfsg dpkg-buildpackage: info: binary-only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20160519-2318 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ rna-star_2.5.2a+dfsg-1_arm64.changes: ───────────────────────────────────── Format: 1.8 Date: Thu, 19 May 2016 18:12:59 +0200 Source: rna-star Binary: rna-star Architecture: arm64 Version: 2.5.2a+dfsg-1 Distribution: yakkety-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: rna-star - ultrafast universal RNA-seq aligner Changes: rna-star (2.5.2a+dfsg-1) unstable; urgency=medium . * New upstream version * Use xz compression option in d/watch * cme fix dpkg-control * Fix homepage * Better hardening Checksums-Sha1: 5425ff760f5b0623ba22d9243b0dde6d7f4edf80 712556 rna-star-dbgsym_2.5.2a+dfsg-1_arm64.ddeb 43d727fb864fcf38b3f8acf0c975d644549674da 335336 rna-star_2.5.2a+dfsg-1_arm64.deb Checksums-Sha256: 6273341d52daa427c4e705b4a375e1e30a9100ed439483c1ee26e6aed64c601c 712556 rna-star-dbgsym_2.5.2a+dfsg-1_arm64.ddeb 4b4fa04726b5c5d80aa01e88eb264604b2fe43b991b2028330419091dace4183 335336 rna-star_2.5.2a+dfsg-1_arm64.deb Files: ba849f7e7b9c66e51f5f8e6bb8c6ed80 712556 science extra rna-star-dbgsym_2.5.2a+dfsg-1_arm64.ddeb 514bdf3724b7b7f03f2b757f7d01447d 335336 science optional rna-star_2.5.2a+dfsg-1_arm64.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ rna-star_2.5.2a+dfsg-1_arm64.deb ──────────────────────────────── new debian package, version 2.0. size 335336 bytes: control archive=1344 bytes. 1451 bytes, 25 lines control 602 bytes, 9 lines md5sums Package: rna-star Version: 2.5.2a+dfsg-1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 723 Depends: libc6 (>= 2.17), libgcc1 (>= 1:3.3.1), libgomp1 (>= 4.9), libhts1 (>= 1.0), libstdc++6 (>= 5.2) Section: science Priority: optional Homepage: https://github.com/alexdobin/STAR/ Description: ultrafast universal RNA-seq aligner Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, the authors experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. drwxr-xr-x root/root 0 2016-05-19 23:18 ./ drwxr-xr-x root/root 0 2016-05-19 23:18 ./usr/ drwxr-xr-x root/root 0 2016-05-19 23:18 ./usr/bin/ -rwxr-xr-x root/root 462040 2016-05-19 23:18 ./usr/bin/STAR drwxr-xr-x root/root 0 2016-05-19 23:18 ./usr/share/ drwxr-xr-x root/root 0 2016-05-19 23:18 ./usr/share/doc-base/ -rw-r--r-- root/root 1179 2016-05-19 16:13 ./usr/share/doc-base/rna-star drwxr-xr-x root/root 0 2016-05-19 23:18 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-05-19 23:18 ./usr/share/doc/rna-star/ -rw-r--r-- root/root 220 2016-05-19 16:13 ./usr/share/doc/rna-star/README.Debian -rw-r--r-- root/root 3196 2016-05-10 21:41 ./usr/share/doc/rna-star/README.md -rw-r--r-- root/root 2119 2016-05-10 21:41 ./usr/share/doc/rna-star/RELEASEnotes.md.gz -rw-r--r-- root/root 251507 2016-05-10 21:41 ./usr/share/doc/rna-star/STARmanual.pdf -rw-r--r-- root/root 733 2016-05-19 16:13 ./usr/share/doc/rna-star/changelog.Debian.gz -rw-r--r-- root/root 2444 2016-05-19 16:13 ./usr/share/doc/rna-star/copyright drwxr-xr-x root/root 0 2016-05-19 23:18 ./usr/share/man/ drwxr-xr-x root/root 0 2016-05-19 23:18 ./usr/share/man/man1/ -rw-r--r-- root/root 814 2016-05-19 23:18 ./usr/share/man/man1/STAR.1.gz ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: arm64 Build-Space: 19752 Build-Time: 253 Distribution: yakkety-proposed Host Architecture: arm64 Install-Time: 20 Job: rna-star_2.5.2a+dfsg-1.dsc Machine Architecture: arm64 Package: rna-star Package-Time: 276 Source-Version: 2.5.2a+dfsg-1 Space: 19752 Status: successful Version: 2.5.2a+dfsg-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20160519-2318 Build needed 00:04:36, 19752k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-9774390'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-9774390/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-9774390'] Unmounting chroot for build PACKAGEBUILD-9774390... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-9774390'] Removing build PACKAGEBUILD-9774390