RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lgw01-04 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 x86_64 Buildd toolchain package versions: launchpad-buildd_140 python-lpbuildd_140 sbuild_0.67.0-2ubuntu7 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3 git-build-recipe_0.3.2 git_1:2.7.4-0ubuntu1 dpkg-dev_1.18.4ubuntu1.1 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.5. Syncing the system clock with the buildd NTP service... 22 Oct 01:41:08 ntpdate[1747]: adjust time server 10.211.37.1 offset -0.005085 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-11057403', '/home/buildd/filecache-default/94f0b0f826e99ad354ce9a7a99ba3c310ddcc327'] Unpacking chroot for build PACKAGEBUILD-11057403 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-11057403'] Mounting chroot for build PACKAGEBUILD-11057403 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-11057403', 'deb http://ftpmaster.internal/ubuntu zesty main universe', 'deb http://ftpmaster.internal/ubuntu zesty-security main universe', 'deb http://ftpmaster.internal/ubuntu zesty-updates main universe', 'deb http://ftpmaster.internal/ubuntu zesty-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-11057403 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-11057403', 'amd64'] Updating debian chroot for build PACKAGEBUILD-11057403 Get:1 http://ftpmaster.internal/ubuntu zesty InRelease [247 kB] Get:2 http://ftpmaster.internal/ubuntu zesty-security InRelease [92.2 kB] Get:3 http://ftpmaster.internal/ubuntu zesty-updates InRelease [92.1 kB] Get:4 http://ftpmaster.internal/ubuntu zesty-proposed InRelease [95.6 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main amd64 Packages [1224 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main Translation-en [583 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/universe amd64 Packages [7739 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/universe Translation-en [4488 kB] Get:9 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 Packages [44.4 kB] Get:10 http://ftpmaster.internal/ubuntu zesty-proposed/main Translation-en [25.9 kB] Get:11 http://ftpmaster.internal/ubuntu zesty-proposed/universe amd64 Packages [243 kB] Get:12 http://ftpmaster.internal/ubuntu zesty-proposed/universe Translation-en [93.6 kB] Fetched 15.0 MB in 5s (2669 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: base-files binutils cpp-6 dmsetup g++-6 gcc-6 gcc-6-base libapparmor1 libasan3 libasn1-8-heimdal libatomic1 libcc1-0 libcilkrts5 libdevmapper1.02.1 libgcc-6-dev libgcc1 libgomp1 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libitm1 libkrb5-26-heimdal liblsan0 liblzma5 libmpx2 libquadmath0 libroken18-heimdal libstdc++-6-dev libstdc++6 libtsan0 libubsan0 libwind0-heimdal linux-libc-dev tzdata xz-utils 37 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 31.2 MB of archives. After this operation, 241 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu zesty/main amd64 base-files amd64 9.6ubuntu6 [55.8 kB] Get:2 http://ftpmaster.internal/ubuntu zesty/main amd64 libquadmath0 amd64 6.2.0-8ubuntu1 [132 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main amd64 libitm1 amd64 6.2.0-8ubuntu1 [27.8 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main amd64 libcc1-0 amd64 6.2.0-8ubuntu1 [31.1 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main amd64 libgomp1 amd64 6.2.0-8ubuntu1 [73.9 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main amd64 libatomic1 amd64 6.2.0-8ubuntu1 [9132 B] Get:7 http://ftpmaster.internal/ubuntu zesty/main amd64 libasan3 amd64 6.2.0-8ubuntu1 [308 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/main amd64 liblsan0 amd64 6.2.0-8ubuntu1 [117 kB] Get:9 http://ftpmaster.internal/ubuntu zesty/main amd64 libtsan0 amd64 6.2.0-8ubuntu1 [260 kB] Get:10 http://ftpmaster.internal/ubuntu zesty/main amd64 libubsan0 amd64 6.2.0-8ubuntu1 [108 kB] Get:11 http://ftpmaster.internal/ubuntu zesty/main amd64 libcilkrts5 amd64 6.2.0-8ubuntu1 [40.9 kB] Get:12 http://ftpmaster.internal/ubuntu zesty/main amd64 libmpx2 amd64 6.2.0-8ubuntu1 [11.4 kB] Get:13 http://ftpmaster.internal/ubuntu zesty/main amd64 gcc-6-base amd64 6.2.0-8ubuntu1 [17.4 kB] Get:14 http://ftpmaster.internal/ubuntu zesty/main amd64 libstdc++6 amd64 6.2.0-8ubuntu1 [401 kB] Get:15 http://ftpmaster.internal/ubuntu zesty/main amd64 g++-6 amd64 6.2.0-8ubuntu1 [7378 kB] Get:16 http://ftpmaster.internal/ubuntu zesty/main amd64 libstdc++-6-dev amd64 6.2.0-8ubuntu1 [1398 kB] Get:17 http://ftpmaster.internal/ubuntu zesty/main amd64 libgcc-6-dev amd64 6.2.0-8ubuntu1 [2306 kB] Get:18 http://ftpmaster.internal/ubuntu zesty/main amd64 gcc-6 amd64 6.2.0-8ubuntu1 [7147 kB] Get:19 http://ftpmaster.internal/ubuntu zesty/main amd64 cpp-6 amd64 6.2.0-8ubuntu1 [6604 kB] Get:20 http://ftpmaster.internal/ubuntu zesty/main amd64 libgcc1 amd64 1:6.2.0-8ubuntu1 [38.0 kB] Get:21 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 binutils amd64 2.27-9ubuntu1 [2418 kB] Get:22 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 liblzma5 amd64 5.2.2-1.2 [91.0 kB] Get:23 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 tzdata all 2016h-1 [169 kB] Get:24 http://ftpmaster.internal/ubuntu zesty/main amd64 libdevmapper1.02.1 amd64 2:1.02.133-1ubuntu1 [164 kB] Get:25 http://ftpmaster.internal/ubuntu zesty/main amd64 dmsetup amd64 2:1.02.133-1ubuntu1 [78.8 kB] Get:26 http://ftpmaster.internal/ubuntu zesty/main amd64 libapparmor1 amd64 2.10.95-4ubuntu5.1 [31.1 kB] Get:27 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libroken18-heimdal amd64 1.7~git20160703+dfsg-1 [41.0 kB] Get:28 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libasn1-8-heimdal amd64 1.7~git20160703+dfsg-1 [174 kB] Get:29 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libheimbase1-heimdal amd64 1.7~git20160703+dfsg-1 [29.2 kB] Get:30 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libhcrypto4-heimdal amd64 1.7~git20160703+dfsg-1 [88.0 kB] Get:31 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libwind0-heimdal amd64 1.7~git20160703+dfsg-1 [47.9 kB] Get:32 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libhx509-5-heimdal amd64 1.7~git20160703+dfsg-1 [107 kB] Get:33 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libkrb5-26-heimdal amd64 1.7~git20160703+dfsg-1 [202 kB] Get:34 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libheimntlm0-heimdal amd64 1.7~git20160703+dfsg-1 [15.1 kB] Get:35 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libgssapi3-heimdal amd64 1.7~git20160703+dfsg-1 [96.7 kB] Get:36 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 xz-utils amd64 5.2.2-1.2 [83.2 kB] Get:37 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 linux-libc-dev amd64 4.8.0-26.28 [854 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 31.2 MB in 4s (6836 kB/s) (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 ... 12312 files and directories currently installed.) Preparing to unpack .../base-files_9.6ubuntu6_amd64.deb ... Unpacking base-files (9.6ubuntu6) over (9.6ubuntu5) ... Setting up base-files (9.6ubuntu6) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (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 ... 12312 files and directories currently installed.) Preparing to unpack .../00-libquadmath0_6.2.0-8ubuntu1_amd64.deb ... Unpacking libquadmath0:amd64 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../01-libitm1_6.2.0-8ubuntu1_amd64.deb ... Unpacking libitm1:amd64 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../02-libcc1-0_6.2.0-8ubuntu1_amd64.deb ... Unpacking libcc1-0:amd64 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../03-libgomp1_6.2.0-8ubuntu1_amd64.deb ... Unpacking libgomp1:amd64 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../04-libatomic1_6.2.0-8ubuntu1_amd64.deb ... Unpacking libatomic1:amd64 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../05-libasan3_6.2.0-8ubuntu1_amd64.deb ... Unpacking libasan3:amd64 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../06-liblsan0_6.2.0-8ubuntu1_amd64.deb ... Unpacking liblsan0:amd64 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../07-libtsan0_6.2.0-8ubuntu1_amd64.deb ... Unpacking libtsan0:amd64 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../08-libubsan0_6.2.0-8ubuntu1_amd64.deb ... Unpacking libubsan0:amd64 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../09-libcilkrts5_6.2.0-8ubuntu1_amd64.deb ... Unpacking libcilkrts5:amd64 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../10-libmpx2_6.2.0-8ubuntu1_amd64.deb ... Unpacking libmpx2:amd64 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../11-gcc-6-base_6.2.0-8ubuntu1_amd64.deb ... Unpacking gcc-6-base:amd64 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Setting up gcc-6-base:amd64 (6.2.0-8ubuntu1) ... (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 ... 12312 files and directories currently installed.) Preparing to unpack .../libstdc++6_6.2.0-8ubuntu1_amd64.deb ... Unpacking libstdc++6:amd64 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Setting up libstdc++6:amd64 (6.2.0-8ubuntu1) ... (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 ... 12312 files and directories currently installed.) Preparing to unpack .../0-g++-6_6.2.0-8ubuntu1_amd64.deb ... Unpacking g++-6 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../1-libstdc++-6-dev_6.2.0-8ubuntu1_amd64.deb ... Unpacking libstdc++-6-dev:amd64 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../2-libgcc-6-dev_6.2.0-8ubuntu1_amd64.deb ... Unpacking libgcc-6-dev:amd64 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../3-gcc-6_6.2.0-8ubuntu1_amd64.deb ... Unpacking gcc-6 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../4-cpp-6_6.2.0-8ubuntu1_amd64.deb ... Unpacking cpp-6 (6.2.0-8ubuntu1) over (6.2.0-5ubuntu12) ... Preparing to unpack .../5-libgcc1_1%3a6.2.0-8ubuntu1_amd64.deb ... Unpacking libgcc1:amd64 (1:6.2.0-8ubuntu1) over (1:6.2.0-5ubuntu12) ... Setting up libgcc1:amd64 (1:6.2.0-8ubuntu1) ... (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 ... 12309 files and directories currently installed.) Preparing to unpack .../0-binutils_2.27-9ubuntu1_amd64.deb ... Unpacking binutils (2.27-9ubuntu1) over (2.27-8ubuntu2) ... Preparing to unpack .../1-liblzma5_5.2.2-1.2_amd64.deb ... Unpacking liblzma5:amd64 (5.2.2-1.2) over (5.1.1alpha+20120614-2.1ubuntu1) ... Setting up liblzma5:amd64 (5.2.2-1.2) ... (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 ... 12309 files and directories currently installed.) Preparing to unpack .../00-tzdata_2016h-1_all.deb ... Unpacking tzdata (2016h-1) over (2016g-1) ... Preparing to unpack .../01-libdevmapper1.02.1_2%3a1.02.133-1ubuntu1_amd64.deb ... Unpacking libdevmapper1.02.1:amd64 (2:1.02.133-1ubuntu1) over (2:1.02.130-1ubuntu1) ... Preparing to unpack .../02-dmsetup_2%3a1.02.133-1ubuntu1_amd64.deb ... Unpacking dmsetup (2:1.02.133-1ubuntu1) over (2:1.02.130-1ubuntu1) ... Preparing to unpack .../03-libapparmor1_2.10.95-4ubuntu5.1_amd64.deb ... Unpacking libapparmor1:amd64 (2.10.95-4ubuntu5.1) over (2.10.95-4ubuntu5) ... Preparing to unpack .../04-libroken18-heimdal_1.7~git20160703+dfsg-1_amd64.deb ... Unpacking libroken18-heimdal:amd64 (1.7~git20160703+dfsg-1) over (1.7~git20150920+dfsg-4ubuntu1) ... Preparing to unpack .../05-libasn1-8-heimdal_1.7~git20160703+dfsg-1_amd64.deb ... Unpacking libasn1-8-heimdal:amd64 (1.7~git20160703+dfsg-1) over (1.7~git20150920+dfsg-4ubuntu1) ... Preparing to unpack .../06-libheimbase1-heimdal_1.7~git20160703+dfsg-1_amd64.deb ... Unpacking libheimbase1-heimdal:amd64 (1.7~git20160703+dfsg-1) over (1.7~git20150920+dfsg-4ubuntu1) ... Preparing to unpack .../07-libhcrypto4-heimdal_1.7~git20160703+dfsg-1_amd64.deb ... Unpacking libhcrypto4-heimdal:amd64 (1.7~git20160703+dfsg-1) over (1.7~git20150920+dfsg-4ubuntu1) ... Preparing to unpack .../08-libwind0-heimdal_1.7~git20160703+dfsg-1_amd64.deb ... Unpacking libwind0-heimdal:amd64 (1.7~git20160703+dfsg-1) over (1.7~git20150920+dfsg-4ubuntu1) ... Preparing to unpack .../09-libhx509-5-heimdal_1.7~git20160703+dfsg-1_amd64.deb ... Unpacking libhx509-5-heimdal:amd64 (1.7~git20160703+dfsg-1) over (1.7~git20150920+dfsg-4ubuntu1) ... Preparing to unpack .../10-libkrb5-26-heimdal_1.7~git20160703+dfsg-1_amd64.deb ... Unpacking libkrb5-26-heimdal:amd64 (1.7~git20160703+dfsg-1) over (1.7~git20150920+dfsg-4ubuntu1) ... Preparing to unpack .../11-libheimntlm0-heimdal_1.7~git20160703+dfsg-1_amd64.deb ... Unpacking libheimntlm0-heimdal:amd64 (1.7~git20160703+dfsg-1) over (1.7~git20150920+dfsg-4ubuntu1) ... Preparing to unpack .../12-libgssapi3-heimdal_1.7~git20160703+dfsg-1_amd64.deb ... Unpacking libgssapi3-heimdal:amd64 (1.7~git20160703+dfsg-1) over (1.7~git20150920+dfsg-4ubuntu1) ... Preparing to unpack .../13-xz-utils_5.2.2-1.2_amd64.deb ... Unpacking xz-utils (5.2.2-1.2) over (5.1.1alpha+20120614-2.1ubuntu1) ... Preparing to unpack .../14-linux-libc-dev_4.8.0-26.28_amd64.deb ... Unpacking linux-libc-dev:amd64 (4.8.0-26.28) over (4.8.0-22.24) ... Setting up libquadmath0:amd64 (6.2.0-8ubuntu1) ... Setting up libgomp1:amd64 (6.2.0-8ubuntu1) ... Setting up libatomic1:amd64 (6.2.0-8ubuntu1) ... Setting up libcc1-0:amd64 (6.2.0-8ubuntu1) ... Setting up libasan3:amd64 (6.2.0-8ubuntu1) ... Setting up libcilkrts5:amd64 (6.2.0-8ubuntu1) ... Setting up tzdata (2016h-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Oct 22 01:41:42 UTC 2016. Universal Time is now: Sat Oct 22 01:41:42 UTC 2016. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libubsan0:amd64 (6.2.0-8ubuntu1) ... Setting up libtsan0:amd64 (6.2.0-8ubuntu1) ... Setting up linux-libc-dev:amd64 (4.8.0-26.28) ... Setting up libroken18-heimdal:amd64 (1.7~git20160703+dfsg-1) ... Setting up libdevmapper1.02.1:amd64 (2:1.02.133-1ubuntu1) ... Setting up liblsan0:amd64 (6.2.0-8ubuntu1) ... Setting up libmpx2:amd64 (6.2.0-8ubuntu1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up libapparmor1:amd64 (2.10.95-4ubuntu5.1) ... Setting up xz-utils (5.2.2-1.2) ... Setting up libheimbase1-heimdal:amd64 (1.7~git20160703+dfsg-1) ... Setting up dmsetup (2:1.02.133-1ubuntu1) ... Setting up binutils (2.27-9ubuntu1) ... Setting up cpp-6 (6.2.0-8ubuntu1) ... Setting up libitm1:amd64 (6.2.0-8ubuntu1) ... Setting up libgcc-6-dev:amd64 (6.2.0-8ubuntu1) ... Setting up libstdc++-6-dev:amd64 (6.2.0-8ubuntu1) ... Setting up libwind0-heimdal:amd64 (1.7~git20160703+dfsg-1) ... Setting up libasn1-8-heimdal:amd64 (1.7~git20160703+dfsg-1) ... Setting up libhcrypto4-heimdal:amd64 (1.7~git20160703+dfsg-1) ... Setting up libhx509-5-heimdal:amd64 (1.7~git20160703+dfsg-1) ... Setting up gcc-6 (6.2.0-8ubuntu1) ... Setting up g++-6 (6.2.0-8ubuntu1) ... Setting up libkrb5-26-heimdal:amd64 (1.7~git20160703+dfsg-1) ... Setting up libheimntlm0-heimdal:amd64 (1.7~git20160703+dfsg-1) ... Setting up libgssapi3-heimdal:amd64 (1.7~git20160703+dfsg-1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-11057403', 'amd64', 'zesty-proposed', '-c', 'chroot:autobuild', '--arch=amd64', '--dist=zesty-proposed', '--purge=never', '--nolog', '-A', 'murasaki_1.68.6-6build2.dsc'] Initiating build PACKAGEBUILD-11057403 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-04.buildd +==============================================================================+ | murasaki 1.68.6-6build2 (amd64) 22 Oct 2016 01:41 | +==============================================================================+ Package: murasaki Version: 1.68.6-6build2 Source Version: 1.68.6-6build2 Distribution: zesty-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/murasaki-CctZXx/murasaki-1.68.6' with '<>' I: NOTICE: Log filtering will replace 'build/murasaki-CctZXx' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-11057403/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- murasaki_1.68.6-6build2.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-PeOD7d/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-PeOD7d/apt_archive ./ InRelease Get:2 copy:/<>/resolver-PeOD7d/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-PeOD7d/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-PeOD7d/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-PeOD7d/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (190 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following 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. Get:1 copy:/<>/resolver-PeOD7d/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 ... 12309 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev Filtered Build-Depends: debhelper (>= 9), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev dpkg-deb: building package 'sbuild-build-depends-murasaki-dummy' in '/<>/resolver-bPtcZK/apt_archive/sbuild-build-depends-murasaki-dummy.deb'. Ign:1 copy:/<>/resolver-bPtcZK/apt_archive ./ InRelease Get:2 copy:/<>/resolver-bPtcZK/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-bPtcZK/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-bPtcZK/apt_archive ./ Sources [278 B] Get:5 copy:/<>/resolver-bPtcZK/apt_archive ./ Packages [599 B] Fetched 2996 B in 0s (219 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install murasaki 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 icu-devtools intltool-debian libarchive-zip-perl libboost-filesystem-dev libboost-filesystem1.61-dev libboost-filesystem1.61.0 libboost-iostreams-dev libboost-iostreams1.61-dev libboost-iostreams1.61.0 libboost-regex-dev libboost-regex1.61-dev libboost-regex1.61.0 libboost-system1.61-dev libboost-system1.61.0 libboost1.61-dev libcroco3 libcrypto++-dev libcrypto++6 libfabric1 libfile-stripnondeterminism-perl libglib2.0-0 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu-dev libicu57 libltdl-dev libltdl7 libmagic1 libnl-3-200 libnl-route-3-200 libnuma-dev libnuma1 libopenmpi-dev libopenmpi2 libpciaccess0 libpipeline1 libpsm-infinipath1 libpstreams-dev librdmacm1 libsigsegv2 libterm-readkey-perl libtext-wrapper-perl libtimedate-perl libtool libunistring0 libxml2 m4 man-db ocl-icd-libopencl1 openmpi-common po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost1.61-doc libboost-atomic1.61-dev libboost-chrono1.61-dev libboost-context1.61-dev libboost-coroutine1.61-dev libboost-date-time1.61-dev libboost-exception1.61-dev libboost-graph1.61-dev libboost-graph-parallel1.61-dev libboost-locale1.61-dev libboost-log1.61-dev libboost-math1.61-dev libboost-mpi1.61-dev libboost-mpi-python1.61-dev libboost-program-options1.61-dev libboost-python1.61-dev libboost-random1.61-dev libboost-serialization1.61-dev libboost-signals1.61-dev libboost-test1.61-dev libboost-thread1.61-dev libboost-timer1.61-dev libboost-wave1.61-dev libboost1.61-tools-dev libmpfrc++-dev libntl-dev libhwloc-contrib-plugins icu-doc libtool-doc openmpi-doc pciutils gfortran | fortran95-compiler gcj-jdk less www-browser opencl-icd libmail-box-perl Recommended packages: curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs openmpi-bin xml-core libmail-sendmail-perl 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 icu-devtools intltool-debian libarchive-zip-perl libboost-filesystem-dev libboost-filesystem1.61-dev libboost-filesystem1.61.0 libboost-iostreams-dev libboost-iostreams1.61-dev libboost-iostreams1.61.0 libboost-regex-dev libboost-regex1.61-dev libboost-regex1.61.0 libboost-system1.61-dev libboost-system1.61.0 libboost1.61-dev libcroco3 libcrypto++-dev libcrypto++6 libfabric1 libfile-stripnondeterminism-perl libglib2.0-0 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu-dev libicu57 libltdl-dev libltdl7 libmagic1 libnl-3-200 libnl-route-3-200 libnuma-dev libnuma1 libopenmpi-dev libopenmpi2 libpciaccess0 libpipeline1 libpsm-infinipath1 libpstreams-dev librdmacm1 libsigsegv2 libterm-readkey-perl libtext-wrapper-perl libtimedate-perl libtool libunistring0 libxml2 m4 man-db ocl-icd-libopencl1 openmpi-common po-debconf sbuild-build-depends-murasaki-dummy 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. Need to get 46.8 MB of archives. After this operation, 310 MB of additional disk space will be used. Get:1 copy:/<>/resolver-bPtcZK/apt_archive ./ sbuild-build-depends-murasaki-dummy 0.invalid.0 [842 B] Get:2 http://ftpmaster.internal/ubuntu zesty/main amd64 groff-base amd64 1.22.3-8 [1142 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main amd64 bsdmainutils amd64 9.0.6ubuntu3 [174 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main amd64 libpipeline1 amd64 1.4.1-2 [24.6 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main amd64 man-db amd64 2.7.5-1 [854 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main amd64 libunistring0 amd64 0.9.3-5.2ubuntu1 [279 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/main amd64 libmagic1 amd64 1:5.28-2ubuntu1 [234 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/main amd64 file amd64 1:5.28-2ubuntu1 [21.7 kB] Get:9 http://ftpmaster.internal/ubuntu zesty/main amd64 gettext-base amd64 0.19.8.1-1ubuntu2 [48.7 kB] Get:10 http://ftpmaster.internal/ubuntu zesty/main amd64 libglib2.0-0 amd64 2.50.0-1 [1140 kB] Get:11 http://ftpmaster.internal/ubuntu zesty/main amd64 libicu57 amd64 57.1-4 [7678 kB] Get:12 http://ftpmaster.internal/ubuntu zesty/main amd64 libnuma1 amd64 2.0.11-1ubuntu2 [21.0 kB] Get:13 http://ftpmaster.internal/ubuntu zesty/main amd64 libxml2 amd64 2.9.4+dfsg1-2 [698 kB] Get:14 http://ftpmaster.internal/ubuntu zesty/main amd64 libsigsegv2 amd64 2.10-5 [14.1 kB] Get:15 http://ftpmaster.internal/ubuntu zesty/main amd64 m4 amd64 1.4.17-5 [195 kB] Get:16 http://ftpmaster.internal/ubuntu zesty/main amd64 autoconf all 2.69-10 [321 kB] Get:17 http://ftpmaster.internal/ubuntu zesty/main amd64 autotools-dev all 20160430.1 [39.6 kB] Get:18 http://ftpmaster.internal/ubuntu zesty/main amd64 automake all 1:1.15-4ubuntu1 [510 kB] Get:19 http://ftpmaster.internal/ubuntu zesty/main amd64 autopoint all 0.19.8.1-1ubuntu2 [412 kB] Get:20 http://ftpmaster.internal/ubuntu zesty/main amd64 libtool all 2.4.6-1 [194 kB] Get:21 http://ftpmaster.internal/ubuntu zesty/main amd64 dh-autoreconf all 12 [15.8 kB] Get:22 http://ftpmaster.internal/ubuntu zesty/main amd64 libarchive-zip-perl all 1.59-1 [84.0 kB] Get:23 http://ftpmaster.internal/ubuntu zesty/main amd64 libfile-stripnondeterminism-perl all 0.028-1 [12.5 kB] Get:24 http://ftpmaster.internal/ubuntu zesty/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:25 http://ftpmaster.internal/ubuntu zesty/main amd64 dh-strip-nondeterminism all 0.028-1 [4820 B] Get:26 http://ftpmaster.internal/ubuntu zesty/main amd64 libcroco3 amd64 0.6.11-1 [81.6 kB] Get:27 http://ftpmaster.internal/ubuntu zesty/main amd64 gettext amd64 0.19.8.1-1ubuntu2 [1083 kB] Get:28 http://ftpmaster.internal/ubuntu zesty/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:29 http://ftpmaster.internal/ubuntu zesty/main amd64 po-debconf all 1.0.19 [234 kB] Get:30 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 debhelper all 10.2.2ubuntu1 [742 kB] Get:31 http://ftpmaster.internal/ubuntu zesty/main amd64 icu-devtools amd64 57.1-4 [169 kB] Get:32 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libboost1.61-dev amd64 1.61.0+dfsg-3 [6821 kB] Get:33 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libboost-system1.61.0 amd64 1.61.0+dfsg-3 [10.2 kB] Get:34 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libboost-filesystem1.61.0 amd64 1.61.0+dfsg-3 [38.5 kB] Get:35 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libboost-system1.61-dev amd64 1.61.0+dfsg-3 [9556 B] Get:36 http://ftpmaster.internal/ubuntu zesty-proposed/universe amd64 libboost-filesystem1.61-dev amd64 1.61.0+dfsg-3 [48.5 kB] Get:37 http://ftpmaster.internal/ubuntu zesty/universe amd64 libboost-filesystem-dev amd64 1.61.0.2 [2896 B] Get:38 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libboost-regex1.61.0 amd64 1.61.0+dfsg-3 [264 kB] Get:39 http://ftpmaster.internal/ubuntu zesty/main amd64 libicu-dev amd64 57.1-4 [16.4 MB] Get:40 http://ftpmaster.internal/ubuntu zesty-proposed/universe amd64 libboost-regex1.61-dev amd64 1.61.0+dfsg-3 [309 kB] Get:41 http://ftpmaster.internal/ubuntu zesty-proposed/main amd64 libboost-iostreams1.61.0 amd64 1.61.0+dfsg-3 [28.3 kB] Get:42 http://ftpmaster.internal/ubuntu zesty-proposed/universe amd64 libboost-iostreams1.61-dev amd64 1.61.0+dfsg-3 [32.8 kB] Get:43 http://ftpmaster.internal/ubuntu zesty/universe amd64 libboost-iostreams-dev amd64 1.61.0.2 [2854 B] Get:44 http://ftpmaster.internal/ubuntu zesty/universe amd64 libboost-regex-dev amd64 1.61.0.2 [3114 B] Get:45 http://ftpmaster.internal/ubuntu zesty/universe amd64 libcrypto++6 amd64 5.6.3-8 [809 kB] Get:46 http://ftpmaster.internal/ubuntu zesty/universe amd64 libcrypto++-dev amd64 5.6.3-8 [1243 kB] Get:47 http://ftpmaster.internal/ubuntu zesty/main amd64 libnl-3-200 amd64 3.2.27-1 [52.1 kB] Get:48 http://ftpmaster.internal/ubuntu zesty/main amd64 libnl-route-3-200 amd64 3.2.27-1 [124 kB] Get:49 http://ftpmaster.internal/ubuntu zesty/main amd64 libibverbs1 amd64 1.2.0-2ubuntu1 [29.3 kB] Get:50 http://ftpmaster.internal/ubuntu zesty/universe amd64 libpsm-infinipath1 amd64 3.3+19.g67c0807.open-3 [170 kB] Get:51 http://ftpmaster.internal/ubuntu zesty/main amd64 librdmacm1 amd64 1.1.0-2 [48.9 kB] Get:52 http://ftpmaster.internal/ubuntu zesty/universe amd64 libfabric1 amd64 1.3.0-2 [199 kB] Get:53 http://ftpmaster.internal/ubuntu zesty/main amd64 libltdl7 amd64 2.4.6-1 [38.6 kB] Get:54 http://ftpmaster.internal/ubuntu zesty/main amd64 libltdl-dev amd64 2.4.6-1 [162 kB] Get:55 http://ftpmaster.internal/ubuntu zesty/main amd64 libpciaccess0 amd64 0.13.4-1 [18.1 kB] Get:56 http://ftpmaster.internal/ubuntu zesty/universe amd64 libpstreams-dev all 0.8.0-2 [106 kB] Get:57 http://ftpmaster.internal/ubuntu zesty/universe amd64 libterm-readkey-perl amd64 2.33-1build1 [27.2 kB] Get:58 http://ftpmaster.internal/ubuntu zesty/universe amd64 libtext-wrapper-perl all 1.05-2 [10.3 kB] Get:59 http://ftpmaster.internal/ubuntu zesty-proposed/universe amd64 openmpi-common all 2.0.1-5ubuntu1 [134 kB] Get:60 http://ftpmaster.internal/ubuntu zesty/universe amd64 libhwloc5 amd64 1.11.3-2 [101 kB] Get:61 http://ftpmaster.internal/ubuntu zesty/main amd64 libnuma-dev amd64 2.0.11-1ubuntu2 [32.1 kB] Get:62 http://ftpmaster.internal/ubuntu zesty/universe amd64 libhwloc-dev amd64 1.11.3-2 [163 kB] Get:63 http://ftpmaster.internal/ubuntu zesty/main amd64 ocl-icd-libopencl1 amd64 2.2.9-2 [30.1 kB] Get:64 http://ftpmaster.internal/ubuntu zesty/universe amd64 libhwloc-plugins amd64 1.11.3-2 [12.2 kB] Get:65 http://ftpmaster.internal/ubuntu zesty/main amd64 libibverbs-dev amd64 1.2.0-2ubuntu1 [84.2 kB] Get:66 http://ftpmaster.internal/ubuntu zesty-proposed/universe amd64 libopenmpi2 amd64 2.0.1-5ubuntu1 [1881 kB] Get:67 http://ftpmaster.internal/ubuntu zesty-proposed/universe amd64 libopenmpi-dev amd64 2.0.1-5ubuntu1 [905 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 46.8 MB in 4s (10.6 MB/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 ... 12309 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-8_amd64.deb ... Unpacking groff-base (1.22.3-8) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_9.0.6ubuntu3_amd64.deb ... Unpacking bsdmainutils (9.0.6ubuntu3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../02-libpipeline1_1.4.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../03-man-db_2.7.5-1_amd64.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package libunistring0:amd64. Preparing to unpack .../04-libunistring0_0.9.3-5.2ubuntu1_amd64.deb ... Unpacking libunistring0:amd64 (0.9.3-5.2ubuntu1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../05-libmagic1_1%3a5.28-2ubuntu1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.28-2ubuntu1) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.28-2ubuntu1_amd64.deb ... Unpacking file (1:5.28-2ubuntu1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.19.8.1-1ubuntu2_amd64.deb ... Unpacking gettext-base (0.19.8.1-1ubuntu2) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../08-libglib2.0-0_2.50.0-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.50.0-1) ... Selecting previously unselected package libicu57:amd64. Preparing to unpack .../09-libicu57_57.1-4_amd64.deb ... Unpacking libicu57:amd64 (57.1-4) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../10-libnuma1_2.0.11-1ubuntu2_amd64.deb ... Unpacking libnuma1:amd64 (2.0.11-1ubuntu2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../11-libxml2_2.9.4+dfsg1-2_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-2) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../12-libsigsegv2_2.10-5_amd64.deb ... Unpacking libsigsegv2:amd64 (2.10-5) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.17-5_amd64.deb ... Unpacking m4 (1.4.17-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-10_all.deb ... Unpacking autoconf (2.69-10) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20160430.1_all.deb ... Unpacking autotools-dev (20160430.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.15-4ubuntu1_all.deb ... Unpacking automake (1:1.15-4ubuntu1) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.19.8.1-1ubuntu2_all.deb ... Unpacking autopoint (0.19.8.1-1ubuntu2) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-1_all.deb ... Unpacking libtool (2.4.6-1) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_12_all.deb ... Unpacking dh-autoreconf (12) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.59-1_all.deb ... Unpacking libarchive-zip-perl (1.59-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_0.028-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (0.028-1) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../22-libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_0.028-1_all.deb ... Unpacking dh-strip-nondeterminism (0.028-1) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../24-libcroco3_0.6.11-1_amd64.deb ... Unpacking libcroco3:amd64 (0.6.11-1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.19.8.1-1ubuntu2_amd64.deb ... Unpacking gettext (0.19.8.1-1ubuntu2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.19_all.deb ... Unpacking po-debconf (1.0.19) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_10.2.2ubuntu1_all.deb ... Unpacking debhelper (10.2.2ubuntu1) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../29-icu-devtools_57.1-4_amd64.deb ... Unpacking icu-devtools (57.1-4) ... Selecting previously unselected package libboost1.61-dev:amd64. Preparing to unpack .../30-libboost1.61-dev_1.61.0+dfsg-3_amd64.deb ... Unpacking libboost1.61-dev:amd64 (1.61.0+dfsg-3) ... Selecting previously unselected package libboost-system1.61.0:amd64. Preparing to unpack .../31-libboost-system1.61.0_1.61.0+dfsg-3_amd64.deb ... Unpacking libboost-system1.61.0:amd64 (1.61.0+dfsg-3) ... Selecting previously unselected package libboost-filesystem1.61.0:amd64. Preparing to unpack .../32-libboost-filesystem1.61.0_1.61.0+dfsg-3_amd64.deb ... Unpacking libboost-filesystem1.61.0:amd64 (1.61.0+dfsg-3) ... Selecting previously unselected package libboost-system1.61-dev:amd64. Preparing to unpack .../33-libboost-system1.61-dev_1.61.0+dfsg-3_amd64.deb ... Unpacking libboost-system1.61-dev:amd64 (1.61.0+dfsg-3) ... Selecting previously unselected package libboost-filesystem1.61-dev:amd64. Preparing to unpack .../34-libboost-filesystem1.61-dev_1.61.0+dfsg-3_amd64.deb ... Unpacking libboost-filesystem1.61-dev:amd64 (1.61.0+dfsg-3) ... Selecting previously unselected package libboost-filesystem-dev:amd64. Preparing to unpack .../35-libboost-filesystem-dev_1.61.0.2_amd64.deb ... Unpacking libboost-filesystem-dev:amd64 (1.61.0.2) ... Selecting previously unselected package libboost-regex1.61.0:amd64. Preparing to unpack .../36-libboost-regex1.61.0_1.61.0+dfsg-3_amd64.deb ... Unpacking libboost-regex1.61.0:amd64 (1.61.0+dfsg-3) ... Selecting previously unselected package libicu-dev. Preparing to unpack .../37-libicu-dev_57.1-4_amd64.deb ... Unpacking libicu-dev (57.1-4) ... Selecting previously unselected package libboost-regex1.61-dev:amd64. Preparing to unpack .../38-libboost-regex1.61-dev_1.61.0+dfsg-3_amd64.deb ... Unpacking libboost-regex1.61-dev:amd64 (1.61.0+dfsg-3) ... Selecting previously unselected package libboost-iostreams1.61.0:amd64. Preparing to unpack .../39-libboost-iostreams1.61.0_1.61.0+dfsg-3_amd64.deb ... Unpacking libboost-iostreams1.61.0:amd64 (1.61.0+dfsg-3) ... Selecting previously unselected package libboost-iostreams1.61-dev:amd64. Preparing to unpack .../40-libboost-iostreams1.61-dev_1.61.0+dfsg-3_amd64.deb ... Unpacking libboost-iostreams1.61-dev:amd64 (1.61.0+dfsg-3) ... Selecting previously unselected package libboost-iostreams-dev:amd64. Preparing to unpack .../41-libboost-iostreams-dev_1.61.0.2_amd64.deb ... Unpacking libboost-iostreams-dev:amd64 (1.61.0.2) ... Selecting previously unselected package libboost-regex-dev:amd64. Preparing to unpack .../42-libboost-regex-dev_1.61.0.2_amd64.deb ... Unpacking libboost-regex-dev:amd64 (1.61.0.2) ... Selecting previously unselected package libcrypto++6. Preparing to unpack .../43-libcrypto++6_5.6.3-8_amd64.deb ... Unpacking libcrypto++6 (5.6.3-8) ... Selecting previously unselected package libcrypto++-dev. Preparing to unpack .../44-libcrypto++-dev_5.6.3-8_amd64.deb ... Unpacking libcrypto++-dev (5.6.3-8) ... Selecting previously unselected package libnl-3-200:amd64. Preparing to unpack .../45-libnl-3-200_3.2.27-1_amd64.deb ... Unpacking libnl-3-200:amd64 (3.2.27-1) ... Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../46-libnl-route-3-200_3.2.27-1_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.2.27-1) ... Selecting previously unselected package libibverbs1. Preparing to unpack .../47-libibverbs1_1.2.0-2ubuntu1_amd64.deb ... Unpacking libibverbs1 (1.2.0-2ubuntu1) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../48-libpsm-infinipath1_3.3+19.g67c0807.open-3_amd64.deb ... Unpacking libpsm-infinipath1 (3.3+19.g67c0807.open-3) ... Selecting previously unselected package librdmacm1. Preparing to unpack .../49-librdmacm1_1.1.0-2_amd64.deb ... Unpacking librdmacm1 (1.1.0-2) ... Selecting previously unselected package libfabric1. Preparing to unpack .../50-libfabric1_1.3.0-2_amd64.deb ... Unpacking libfabric1 (1.3.0-2) ... Selecting previously unselected package libltdl7:amd64. Preparing to unpack .../51-libltdl7_2.4.6-1_amd64.deb ... Unpacking libltdl7:amd64 (2.4.6-1) ... Selecting previously unselected package libltdl-dev:amd64. Preparing to unpack .../52-libltdl-dev_2.4.6-1_amd64.deb ... Unpacking libltdl-dev:amd64 (2.4.6-1) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../53-libpciaccess0_0.13.4-1_amd64.deb ... Unpacking libpciaccess0:amd64 (0.13.4-1) ... Selecting previously unselected package libpstreams-dev. Preparing to unpack .../54-libpstreams-dev_0.8.0-2_all.deb ... Unpacking libpstreams-dev (0.8.0-2) ... Selecting previously unselected package libterm-readkey-perl. Preparing to unpack .../55-libterm-readkey-perl_2.33-1build1_amd64.deb ... Unpacking libterm-readkey-perl (2.33-1build1) ... Selecting previously unselected package libtext-wrapper-perl. Preparing to unpack .../56-libtext-wrapper-perl_1.05-2_all.deb ... Unpacking libtext-wrapper-perl (1.05-2) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../57-openmpi-common_2.0.1-5ubuntu1_all.deb ... Unpacking openmpi-common (2.0.1-5ubuntu1) ... Selecting previously unselected package libhwloc5:amd64. Preparing to unpack .../58-libhwloc5_1.11.3-2_amd64.deb ... Unpacking libhwloc5:amd64 (1.11.3-2) ... Selecting previously unselected package libnuma-dev:amd64. Preparing to unpack .../59-libnuma-dev_2.0.11-1ubuntu2_amd64.deb ... Unpacking libnuma-dev:amd64 (2.0.11-1ubuntu2) ... Selecting previously unselected package libhwloc-dev:amd64. Preparing to unpack .../60-libhwloc-dev_1.11.3-2_amd64.deb ... Unpacking libhwloc-dev:amd64 (1.11.3-2) ... Selecting previously unselected package ocl-icd-libopencl1:amd64. Preparing to unpack .../61-ocl-icd-libopencl1_2.2.9-2_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.2.9-2) ... Selecting previously unselected package libhwloc-plugins. Preparing to unpack .../62-libhwloc-plugins_1.11.3-2_amd64.deb ... Unpacking libhwloc-plugins (1.11.3-2) ... Selecting previously unselected package libibverbs-dev. Preparing to unpack .../63-libibverbs-dev_1.2.0-2ubuntu1_amd64.deb ... Unpacking libibverbs-dev (1.2.0-2ubuntu1) ... Selecting previously unselected package libopenmpi2. Preparing to unpack .../64-libopenmpi2_2.0.1-5ubuntu1_amd64.deb ... Unpacking libopenmpi2 (2.0.1-5ubuntu1) ... Selecting previously unselected package libopenmpi-dev. Preparing to unpack .../65-libopenmpi-dev_2.0.1-5ubuntu1_amd64.deb ... Unpacking libopenmpi-dev (2.0.1-5ubuntu1) ... Selecting previously unselected package sbuild-build-depends-murasaki-dummy. Preparing to unpack .../66-sbuild-build-depends-murasaki-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-murasaki-dummy (0.invalid.0) ... Setting up libpstreams-dev (0.8.0-2) ... Setting up libboost-system1.61.0:amd64 (1.61.0+dfsg-3) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up libcrypto++6 (5.6.3-8) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:amd64 (2.10-5) ... Setting up libcrypto++-dev (5.6.3-8) ... Setting up libnuma1:amd64 (2.0.11-1ubuntu2) ... Setting up groff-base (1.22.3-8) ... Setting up libglib2.0-0:amd64 (2.50.0-1) ... No schema files found: doing nothing. Setting up libboost-iostreams1.61.0:amd64 (1.61.0+dfsg-3) ... Setting up gettext-base (0.19.8.1-1ubuntu2) ... Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up m4 (1.4.17-5) ... Setting up libicu57:amd64 (57.1-4) ... Setting up libboost1.61-dev:amd64 (1.61.0+dfsg-3) ... Setting up libxml2:amd64 (2.9.4+dfsg1-2) ... Setting up libterm-readkey-perl (2.33-1build1) ... Setting up libmagic1:amd64 (1:5.28-2ubuntu1) ... Setting up libcroco3:amd64 (0.6.11-1) ... Setting up libpsm-infinipath1 (3.3+19.g67c0807.open-3) ... Setting up libboost-filesystem1.61.0:amd64 (1.61.0+dfsg-3) ... Setting up libtext-wrapper-perl (1.05-2) ... Setting up openmpi-common (2.0.1-5ubuntu1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up autotools-dev (20160430.1) ... Setting up libunistring0:amd64 (0.9.3-5.2ubuntu1) ... Setting up libltdl7:amd64 (2.4.6-1) ... Setting up libpciaccess0:amd64 (0.13.4-1) ... Setting up icu-devtools (57.1-4) ... Setting up libnuma-dev:amd64 (2.0.11-1ubuntu2) ... Setting up ocl-icd-libopencl1:amd64 (2.2.9-2) ... 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 libnl-3-200:amd64 (3.2.27-1) ... Setting up autopoint (0.19.8.1-1ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.028-1) ... Setting up libboost-system1.61-dev:amd64 (1.61.0+dfsg-3) ... Setting up libltdl-dev:amd64 (2.4.6-1) ... Setting up libboost-regex1.61.0:amd64 (1.61.0+dfsg-3) ... Setting up gettext (0.19.8.1-1ubuntu2) ... Setting up libnl-route-3-200:amd64 (3.2.27-1) ... Setting up autoconf (2.69-10) ... Setting up libicu-dev (57.1-4) ... Setting up file (1:5.28-2ubuntu1) ... Setting up libhwloc5:amd64 (1.11.3-2) ... Setting up libhwloc-plugins (1.11.3-2) ... Setting up libboost-filesystem1.61-dev:amd64 (1.61.0+dfsg-3) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libboost-regex1.61-dev:amd64 (1.61.0+dfsg-3) ... 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 man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-regex-dev:amd64 (1.61.0.2) ... Setting up libtool (2.4.6-1) ... Setting up libibverbs1 (1.2.0-2ubuntu1) ... Setting up libboost-iostreams1.61-dev:amd64 (1.61.0+dfsg-3) ... Setting up po-debconf (1.0.19) ... Setting up libhwloc-dev:amd64 (1.11.3-2) ... Setting up librdmacm1 (1.1.0-2) ... Setting up libboost-filesystem-dev:amd64 (1.61.0.2) ... Setting up libboost-iostreams-dev:amd64 (1.61.0.2) ... Setting up libibverbs-dev (1.2.0-2ubuntu1) ... Setting up libfabric1 (1.3.0-2) ... Setting up libopenmpi2 (2.0.1-5ubuntu1) ... Setting up libopenmpi-dev (2.0.1-5ubuntu1) ... update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode Setting up dh-autoreconf (12) ... Setting up dh-strip-nondeterminism (0.028-1) ... Setting up debhelper (10.2.2ubuntu1) ... Setting up sbuild-build-depends-murasaki-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-45-generic amd64 (x86_64) Toolchain package versions: binutils_2.27-9ubuntu1 dpkg-dev_1.18.10ubuntu1 g++-6_6.2.0-8ubuntu1 gcc-6_6.2.0-8ubuntu1 libc6-dev_2.24-3ubuntu1 libstdc++-6-dev_6.2.0-8ubuntu1 libstdc++6_6.2.0-8ubuntu1 linux-libc-dev_4.8.0-26.28 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.3.1 apt-transport-https_1.3.1 autoconf_2.69-10 automake_1:1.15-4ubuntu1 autopoint_0.19.8.1-1ubuntu2 autotools-dev_20160430.1 base-files_9.6ubuntu6 base-passwd_3.5.40 bash_4.3-15ubuntu1 binutils_2.27-9ubuntu1 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.28.2-1ubuntu1 build-essential_12.1ubuntu2 bzip2_1.0.6-8build1 ca-certificates_20160104ubuntu1 coreutils_8.25-2ubuntu2 cpp_4:6.1.1-1ubuntu2 cpp-6_6.2.0-8ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.59ubuntu1 debhelper_10.2.2ubuntu1 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.3-3 dmsetup_2:1.02.133-1ubuntu1 dpkg_1.18.10ubuntu1 dpkg-dev_1.18.10ubuntu1 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-1ubuntu2 file_1:5.28-2ubuntu1 findutils_4.6.0+git+20160703-2 g++_4:6.1.1-1ubuntu2 g++-6_6.2.0-8ubuntu1 gcc_4:6.1.1-1ubuntu2 gcc-6_6.2.0-8ubuntu1 gcc-6-base_6.2.0-8ubuntu1 gettext_0.19.8.1-1ubuntu2 gettext-base_0.19.8.1-1ubuntu2 gnupg_2.1.15-1ubuntu6 gnupg-agent_2.1.15-1ubuntu6 gpgv_2.1.15-1ubuntu6 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-4ubuntu1 hostname_3.18 icu-devtools_57.1-4 init_1.45 init-system-helpers_1.45 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapparmor1_2.10.95-4ubuntu5.1 libapt-pkg5.0_1.3.1 libarchive-zip-perl_1.59-1 libasan3_6.2.0-8ubuntu1 libasn1-8-heimdal_1.7~git20160703+dfsg-1 libassuan0_2.4.3-1 libatomic1_6.2.0-8ubuntu1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1ubuntu1 libaudit1_1:2.6.6-1ubuntu1 libblkid1_2.28.2-1ubuntu1 libboost-filesystem-dev_1.61.0.2 libboost-filesystem1.61-dev_1.61.0+dfsg-3 libboost-filesystem1.61.0_1.61.0+dfsg-3 libboost-iostreams-dev_1.61.0.2 libboost-iostreams1.61-dev_1.61.0+dfsg-3 libboost-iostreams1.61.0_1.61.0+dfsg-3 libboost-regex-dev_1.61.0.2 libboost-regex1.61-dev_1.61.0+dfsg-3 libboost-regex1.61.0_1.61.0+dfsg-3 libboost-system1.61-dev_1.61.0+dfsg-3 libboost-system1.61.0_1.61.0+dfsg-3 libboost1.61-dev_1.61.0+dfsg-3 libbz2-1.0_1.0.6-8build1 libc-bin_2.24-3ubuntu1 libc-dev-bin_2.24-3ubuntu1 libc6_2.24-3ubuntu1 libc6-dev_2.24-3ubuntu1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_6.2.0-8ubuntu1 libcilkrts5_6.2.0-8ubuntu1 libcomerr2_1.43.3-1 libcroco3_0.6.11-1 libcrypto++-dev_5.6.3-8 libcrypto++6_5.6.3-8 libcryptsetup4_2:1.7.2-0ubuntu1 libcurl3-gnutls_7.50.1-1ubuntu1 libdb5.3_5.3.28-12 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.133-1ubuntu1 libdpkg-perl_1.18.10ubuntu1 libfabric1_1.3.0-2 libfakeroot_1.21-1ubuntu2 libfdisk1_2.28.2-1ubuntu1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libgcc-6-dev_6.2.0-8ubuntu1 libgcc1_1:6.2.0-8ubuntu1 libgcrypt20_1.7.2-2ubuntu1 libgdbm3_1.8.3-14 libglib2.0-0_2.50.0-1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.3-5ubuntu1 libgomp1_6.2.0-8ubuntu1 libgpg-error0_1.24-1 libgssapi-krb5-2_1.14.3+dfsg-2 libgssapi3-heimdal_1.7~git20160703+dfsg-1 libhcrypto4-heimdal_1.7~git20160703+dfsg-1 libheimbase1-heimdal_1.7~git20160703+dfsg-1 libheimntlm0-heimdal_1.7~git20160703+dfsg-1 libhogweed4_3.2-1 libhwloc-dev_1.11.3-2 libhwloc-plugins_1.11.3-2 libhwloc5_1.11.3-2 libhx509-5-heimdal_1.7~git20160703+dfsg-1 libibverbs-dev_1.2.0-2ubuntu1 libibverbs1_1.2.0-2ubuntu1 libicu-dev_57.1-4 libicu57_57.1-4 libidn11_1.33-1 libip4tc0_1.6.0-3ubuntu2 libisl15_0.17.1-1 libitm1_6.2.0-8ubuntu1 libk5crypto3_1.14.3+dfsg-2 libkeyutils1_1.5.9-9ubuntu1 libkmod2_22-1.1ubuntu1 libkrb5-26-heimdal_1.7~git20160703+dfsg-1 libkrb5-3_1.14.3+dfsg-2 libkrb5support0_1.14.3+dfsg-2 libksba8_1.3.4-4 libldap-2.4-2_2.4.42+dfsg-2ubuntu4 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblsan0_6.2.0-8ubuntu1 libltdl-dev_2.4.6-1 libltdl7_2.4.6-1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.2 libmagic1_1:5.28-2ubuntu1 libmount1_2.28.2-1ubuntu1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libmpx2_6.2.0-8ubuntu1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.2-1 libnl-3-200_3.2.27-1 libnl-route-3-200_3.2.27-1 libnpth0_1.2-3 libnuma-dev_2.0.11-1ubuntu2 libnuma1_2.0.11-1ubuntu2 libopenmpi-dev_2.0.1-5ubuntu1 libopenmpi2_2.0.1-5ubuntu1 libp11-kit0_0.23.2-5 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 libpciaccess0_0.13.4-1 libpcre3_2:8.39-2 libperl5.22_5.22.2-3 libpipeline1_1.4.1-2 libpng16-16_1.6.25-1 libprocps6_2:3.3.12-1ubuntu2 libpsm-infinipath1_3.3+19.g67c0807.open-3 libpstreams-dev_0.8.0-2 libquadmath0_6.2.0-8ubuntu1 librdmacm1_1.1.0-2 libreadline7_7.0-0ubuntu2 libroken18-heimdal_1.7~git20160703+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_2.3.1-2ubuntu2 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_2.28.2-1ubuntu1 libsqlite3-0_3.14.1-1build1 libss2_1.43.3-1 libssl1.0.0_1.0.2g-1ubuntu9 libstdc++-6-dev_6.2.0-8ubuntu1 libstdc++6_6.2.0-8ubuntu1 libsystemd0_231-9git1 libtasn1-6_4.9-4 libterm-readkey-perl_2.33-1build1 libtext-wrapper-perl_1.05-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-1 libtsan0_6.2.0-8ubuntu1 libubsan0_6.2.0-8ubuntu1 libudev1_231-9git1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28.2-1ubuntu1 libwind0-heimdal_1.7~git20160703+dfsg-1 libxml2_2.9.4+dfsg1-2 linux-libc-dev_4.8.0-26.28 lockfile-progs_0.1.17 login_1:4.2-3.2ubuntu1 lsb-base_9.20160110ubuntu5 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mount_2.28.2-1ubuntu1 multiarch-support_2.24-3ubuntu1 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 ocl-icd-libopencl1_2.2.9-2 openmpi-common_2.0.1-5ubuntu1 openssl_1.0.2g-1ubuntu9 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu1 patch_2.7.5-1 perl_5.22.2-3 perl-base_5.22.2-3 perl-modules-5.22_5.22.2-3 pinentry-curses_0.9.7-5 pkg-create-dbgsym_0.72 pkgbinarymangler_131 po-debconf_1.0.19 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-murasaki-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 systemd_231-9git1 systemd-sysv_231-9git1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-1 tzdata_2016h-1 ubuntu-keyring_2016.09.19 util-linux_2.28.2-1ubuntu1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2ubuntu5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Oct 22 01:40:00 2016 UTC gpgv: using RSA key gpgv: issuer "steve.langasek@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./murasaki_1.68.6-6build2.dsc dpkg-source: info: extracting murasaki in murasaki-1.68.6 dpkg-source: info: unpacking murasaki_1.68.6.orig.tar.gz dpkg-source: info: unpacking murasaki_1.68.6-6build2.debian.tar.xz dpkg-source: info: applying use_proper_libboost_names.patch dpkg-source: info: applying include_libpstream.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying man_syntax.patch dpkg-source: info: applying freebsd.patch dpkg-source: info: applying gcc-6.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=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=/<> SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package murasaki dpkg-buildpackage: info: source version 1.68.6-6build2 dpkg-buildpackage: info: source distribution zesty dpkg-source --before-build murasaki-1.68.6 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean make -j1 clean make[1]: Entering directory '/<>' rm -rf *.o *~ .*~ core make -C src clean make[2]: Entering directory '/<>/src' rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' dh_clean debian/rules build dh build dh_testdir dh_update_autotools_config dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- USE_MPI=YES make -j1 USE_MPI=YES make[2]: Entering directory '/<>' make -C src all make[3]: Entering directory '/<>/src' mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c murasaki.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki.cc:37: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki.cc:37: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki.cc:37: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ murasaki.cc: In function ‘void procLocs(LocList&, std::__cxx11::list&, int, int)’: murasaki.cc:1008:8: warning: variable ‘revZero’ set but not used [-Wunused-but-set-variable] bool revZero=false; ^~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c timing.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c dinkymath.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from dinkymath.cc:27: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from dinkymath.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from dinkymath.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ dinkymath.cc: In function ‘std::__cxx11::string littleEndianStr(unsigned int, int)’: dinkymath.cc:40:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] int last=0; ^~~~ dinkymath.cc: In function ‘std::__cxx11::string littleEndianPat(unsigned int, int)’: dinkymath.cc:53:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] int last=0; ^~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c sequence.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from sequence.cc:28: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from sequence.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from sequence.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ sequence.cc: In destructor ‘Sequence::~Sequence()’: sequence.cc:377:123: warning: throw will always call terminate() [-Wterminate] throw MurasakiException("Couldn't mark System V IPC shared memory region for deletion for sequence "+name+strerror(errno)); ^ sequence.cc:377:123: note: in C++11 destructors default to noexcept sequence.cc: In destructor ‘BitSequence::~BitSequence()’: sequence.cc:1394:133: warning: throw will always call terminate() [-Wterminate] throw MurasakiException("Couldn't detach System V shared memory region for "+(seq ? seq->filename:string("(anon)"))+strerror(errno)); ^ sequence.cc:1394:133: note: in C++11 destructors default to noexcept sequence.cc: In member function ‘std::pair IntervalSet::entropy() const’: sequence.cc:3332:10: warning: variable ‘shortest’ set but not used [-Wunused-but-set-variable] SeqPos shortest=0,shortlen=length(spaces[0]); ^~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c msethash.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from msethash.cc:25: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from msethash.cc:25: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from msethash.cc:25: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c options.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from options.h:28, from options.cc:26: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from options.h:28, from options.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from options.h:28, from options.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecohash.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecolist.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecolist.cc:20: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecolist.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecolist.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c murasaki_mpi.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki_mpi.cc:33: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki_mpi.cc:33: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki_mpi.cc:33: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ murasaki_mpi.cc: In function ‘void mpi_types_init()’: murasaki_mpi.cc:107:3: warning: ‘int MPI_Address(void*, MPI_Aint*)’ is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.key,disp); ^~~~~~~~~~~ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1200:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:107:28: warning: ‘int MPI_Address(void*, MPI_Aint*)’ is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.key,disp); ^ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1200:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:108:3: warning: ‘int MPI_Address(void*, MPI_Aint*)’ is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.seqno,disp+1); ^~~~~~~~~~~ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1200:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:108:32: warning: ‘int MPI_Address(void*, MPI_Aint*)’ is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.seqno,disp+1); ^ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1200:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:109:3: warning: ‘int MPI_Address(void*, MPI_Aint*)’ is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.pos,disp+1); ^~~~~~~~~~~ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1200:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:109:30: warning: ‘int MPI_Address(void*, MPI_Aint*)’ is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.pos,disp+1); ^ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1200:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:112:3: warning: ‘int MPI_Type_struct(int, int*, MPI_Aint*, ompi_datatype_t**, ompi_datatype_t**)’ is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(3,blocklen,disp,type,&MPI_HashMessage_type); ^~~~~~~~~~~~~~~ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1817:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ murasaki_mpi.cc:112:61: warning: ‘int MPI_Type_struct(int, int*, MPI_Aint*, ompi_datatype_t**, ompi_datatype_t**)’ is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(3,blocklen,disp,type,&MPI_HashMessage_type); ^ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1817:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ murasaki_mpi.cc: In function ‘void mpi_hasher_client_mode(BitSequence*)’: murasaki_mpi.cc:561:9: warning: variable ‘send_done’ set but not used [-Wunused-but-set-variable] int send_done; ^~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c arrayhash.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from arrayhash.cc:28: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from arrayhash.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from arrayhash.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c seqread.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from seqread.cc:28: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from seqread.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from seqread.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c scoring.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from scoring.cc:27: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from scoring.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from scoring.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c openhash.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from openhash.h:29, from openhash.cc:26: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from openhash.h:29, from openhash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from openhash.h:29, from openhash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c genopts.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c binseq.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from binseq.cc:21: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from binseq.cc:21: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from binseq.cc:21: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-image.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-image.cc:33: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-image.cc:33: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-image.cc:33: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr.cc cgr.cc: In member function ‘void Cgr::merge(Cgr&)’: cgr.cc:140:7: warning: variable ‘redist’ set but not used [-Wunused-but-set-variable] int redist=(unsigned long)(rez*rez)<=seedcount; ^~~~~~ cgr.cc: In member function ‘bool Cgr::savePNG(std::__cxx11::string)’: cgr.cc:288:7: warning: variable ‘res’ set but not used [-Wunused-but-set-variable] int res; ^~~ cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::__cxx11::string)’: cgr.cc:435:7: warning: variable ‘wordwidth’ set but not used [-Wunused-but-set-variable] int wordwidth=1; ^~~~~~~~~ cgr.cc: In member function ‘int PgmBuffer::loadBinaryPGM(std::__cxx11::string)’: cgr.cc:546:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] data.push_back(*(gray*)(line)); ^ cgr.cc:557:31: warning: ‘height’ may be used uninitialized in this function [-Wmaybe-uninitialized] if(data.size()<(uint)(height*width)) ~~~~~~~^~~~~~~ cgr.cc:557:31: warning: ‘width’ may be used uninitialized in this function [-Wmaybe-uninitialized] cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::__cxx11::string)’: cgr.cc:485:31: warning: ‘height’ may be used uninitialized in this function [-Wmaybe-uninitialized] if(data.size()<(uint)(height*width)) ~~~~~~~^~~~~~~ cgr.cc:485:31: warning: ‘width’ may be used uninitialized in this function [-Wmaybe-uninitialized] mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-compare.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-random.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-sample.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-sample.cc:35: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-sample.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-sample.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ cgr-sample.cc: In function ‘int main(int, char**)’: cgr-sample.cc:54:8: warning: variable ‘repeatmask’ set but not used [-Wunused-but-set-variable] bool repeatmask=false,save=false; ^~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c testeco.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from testeco.cc:20: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from testeco.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from testeco.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-compare.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-or.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c geneparse.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from geneparse.cc:30: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from geneparse.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from geneparse.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-and.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-best.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-coverage.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from align-coverage.cc:35: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from align-coverage.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from align-coverage.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ align-coverage.cc: In function ‘int main(int, char**)’: align-coverage.cc:148:10: warning: variable ‘seqStats’ set but not used [-Wunused-but-set-variable] bool seqStats=true; ^~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c getsegments.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from getsegments.cc:30: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from getsegments.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from getsegments.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c mbfa.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from mbfa.cc:30: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from mbfa.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from mbfa.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' for bin in geneparse mbfa murasaki cgr-* testeco align-* ; do \ mv ${bin} ${bin}-mpi ; \ done make clean make[2]: Entering directory '/<>' rm -rf *.o *~ .*~ core make -C src clean make[3]: Entering directory '/<>/src' rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' dh_auto_build -- USE_MPI=NO make -j1 USE_MPI=NO make[2]: Entering directory '/<>' make -C src all make[3]: Entering directory '/<>/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki.cc:37: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki.cc:37: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki.cc:37: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ murasaki.cc: In function ‘void procLocs(LocList&, std::__cxx11::list&, int, int)’: murasaki.cc:1008:8: warning: variable ‘revZero’ set but not used [-Wunused-but-set-variable] bool revZero=false; ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c timing.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c dinkymath.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from dinkymath.cc:27: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from dinkymath.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from dinkymath.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ dinkymath.cc: In function ‘std::__cxx11::string littleEndianStr(unsigned int, int)’: dinkymath.cc:40:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] int last=0; ^~~~ dinkymath.cc: In function ‘std::__cxx11::string littleEndianPat(unsigned int, int)’: dinkymath.cc:53:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] int last=0; ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c sequence.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from sequence.cc:28: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from sequence.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from sequence.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ sequence.cc: In member function ‘std::pair IntervalSet::entropy() const’: sequence.cc:3332:10: warning: variable ‘shortest’ set but not used [-Wunused-but-set-variable] SeqPos shortest=0,shortlen=length(spaces[0]); ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c msethash.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from msethash.cc:25: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from msethash.cc:25: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from msethash.cc:25: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c options.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from options.h:28, from options.cc:26: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from options.h:28, from options.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from options.h:28, from options.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c ecohash.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c ecolist.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecolist.cc:20: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecolist.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecolist.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki_mpi.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c arrayhash.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from arrayhash.cc:28: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from arrayhash.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from arrayhash.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c seqread.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from seqread.cc:28: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from seqread.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from seqread.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c scoring.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from scoring.cc:27: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from scoring.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from scoring.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c openhash.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from openhash.h:29, from openhash.cc:26: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from openhash.h:29, from openhash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from openhash.h:29, from openhash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c genopts.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c binseq.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from binseq.cc:21: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from binseq.cc:21: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from binseq.cc:21: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-image.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-image.cc:33: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-image.cc:33: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-image.cc:33: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr.cc cgr.cc: In member function ‘void Cgr::merge(Cgr&)’: cgr.cc:140:7: warning: variable ‘redist’ set but not used [-Wunused-but-set-variable] int redist=(unsigned long)(rez*rez)<=seedcount; ^~~~~~ cgr.cc: In member function ‘bool Cgr::savePNG(std::__cxx11::string)’: cgr.cc:288:7: warning: variable ‘res’ set but not used [-Wunused-but-set-variable] int res; ^~~ cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::__cxx11::string)’: cgr.cc:435:7: warning: variable ‘wordwidth’ set but not used [-Wunused-but-set-variable] int wordwidth=1; ^~~~~~~~~ cgr.cc: In member function ‘int PgmBuffer::loadBinaryPGM(std::__cxx11::string)’: cgr.cc:546:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] data.push_back(*(gray*)(line)); ^ cgr.cc:557:31: warning: ‘height’ may be used uninitialized in this function [-Wmaybe-uninitialized] if(data.size()<(uint)(height*width)) ~~~~~~~^~~~~~~ cgr.cc:557:31: warning: ‘width’ may be used uninitialized in this function [-Wmaybe-uninitialized] cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::__cxx11::string)’: cgr.cc:485:31: warning: ‘height’ may be used uninitialized in this function [-Wmaybe-uninitialized] if(data.size()<(uint)(height*width)) ~~~~~~~^~~~~~~ cgr.cc:485:31: warning: ‘width’ may be used uninitialized in this function [-Wmaybe-uninitialized] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-compare.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-random.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-sample.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-sample.cc:35: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-sample.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-sample.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ cgr-sample.cc: In function ‘int main(int, char**)’: cgr-sample.cc:54:8: warning: variable ‘repeatmask’ set but not used [-Wunused-but-set-variable] bool repeatmask=false,save=false; ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c testeco.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from testeco.cc:20: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from testeco.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from testeco.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-compare.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c alignments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-or.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c geneparse.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from geneparse.cc:30: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from geneparse.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from geneparse.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-and.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-best.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-coverage.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from align-coverage.cc:35: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from align-coverage.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from align-coverage.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ align-coverage.cc: In function ‘int main(int, char**)’: align-coverage.cc:148:10: warning: variable ‘seqStats’ set but not used [-Wunused-but-set-variable] bool seqStats=true; ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c getsegments.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from getsegments.cc:30: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from getsegments.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from getsegments.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c mbfa.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from mbfa.cc:30: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from mbfa.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from mbfa.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install debian/rules override_dh_install-arch make[1]: Entering directory '/<>' dh_install -a # using wildcards in install files is practical but it duplicates some files find debian/murasaki/usr -name "*-mpi" -delete make[1]: Leaving directory '/<>' dh_install -Nmurasaki -Nmurasaki-mpi dh_installdocs dh_installchangelogs debian/rules override_dh_installman-indep make[1]: Entering directory '/<>' dh_installman -i # create manpages for PL files mkdir -p debian/murasaki-common/usr/share/man/man1 for pscript in debian/murasaki-common/usr/lib/debian-med/bin/* ; do \ pod2man ${pscript} > debian/murasaki-common/usr/share/man/man1/`basename ${pscript}`.1 ; \ done pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/anchors2maf.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/anchors2osfinder.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/antisense.pl debian/murasaki-common/usr/lib/debian-med/bin/chromostitch.pl around line 134: '=item' outside of any '=over' debian/murasaki-common/usr/lib/debian-med/bin/chromostitch.pl around line 141: You forgot a '=back' before '=head1' POD document had syntax errors at /usr/bin/pod2man line 68. pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/dna2binary.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/dnashuffle.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/geneparse.pl debian/murasaki-common/usr/lib/debian-med/bin/getcds.pl around line 646: '=item' outside of any '=over' debian/murasaki-common/usr/lib/debian-med/bin/getcds.pl around line 646: =over without closing =back POD document had syntax errors at /usr/bin/pod2man line 68. pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/humantime.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/osfinder2anchors.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/randpat.pl find debian/murasaki-common/usr/share/man/man1 -empty -delete make[1]: Leaving directory '/<>' dh_installman -Nmurasaki-common dh_perl debian/rules override_dh_link make[1]: Entering directory '/<>' dh_link mkdir -p debian/murasaki-mpi/usr/share/man/man1 for man in debian/murasaki/usr/share/man/man1/* ; do \ ln -s `basename ${man}`.gz debian/murasaki-mpi/usr/share/man/man1/`basename ${man} .1`-mpi.1.gz ; \ done make[1]: Leaving directory '/<>' dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms-indep make[1]: Entering directory '/<>' dh_fixperms -i chmod a+x debian/murasaki-common/usr/share/perl5/murasaki/config.pl make[1]: Leaving directory '/<>' dh_fixperms -Nmurasaki-common dh_strip dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform amd64: murasaki murasaki-mpi dh_strip debug symbol extraction: packages to act on: murasaki murasaki-mpi dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package murasaki-mpi: unused substitution variable ${perl:Depends} /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package murasaki-mpi: unused substitution variable ${perl:Depends} dpkg-gencontrol: warning: Depends field of package murasaki-common: unknown substitution variable ${misc:perl} dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package murasaki-common: unused substitution variable ${perl:Depends} dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform amd64: murasaki murasaki-mpi dh_gencontrol debug symbol wrapper: packages to act on: murasaki murasaki-mpi dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package murasaki (pkgdir debian/murasaki, ddeb package dir debian/murasaki-dbgsym) dh_gencontrol debug symbol wrapper: building murasaki-dbgsym_1.68.6-6build2_amd64.ddeb dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-6build2_amd64.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile murasaki-dbgsym_1.68.6-6build2_amd64.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: processing package murasaki-mpi (pkgdir debian/murasaki-mpi, ddeb package dir debian/murasaki-mpi-dbgsym) dh_gencontrol debug symbol wrapper: building murasaki-mpi-dbgsym_1.68.6-6build2_amd64.ddeb dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-6build2_amd64.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile murasaki-mpi-dbgsym_1.68.6-6build2_amd64.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums dh_builddeb INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 pkgstriptranslations: processing murasaki-mpi (in debian/murasaki-mpi); do_strip: , oemstrip: pkgstriptranslations: processing murasaki (in debian/murasaki); do_strip: , oemstrip: pkgstriptranslations: processing murasaki-common (in debian/murasaki-common); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/murasaki/DEBIAN/control, package murasaki, directory debian/murasaki pkgstripfiles: processing control file: debian/murasaki-mpi/DEBIAN/control, package murasaki-mpi, directory debian/murasaki-mpi Skipping arch: any to arch: all dependency to murasaki-common pkgstripfiles: Running PNG optimization (using 4 cpus) for package murasaki ... Skipping arch: any to arch: all dependency to murasaki-common pkgstripfiles: No PNG files. dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-6build2_amd64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package murasaki-mpi ... pkgstripfiles: No PNG files. dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-6build2_amd64.deb'. pkgstripfiles: processing control file: debian/murasaki-common/DEBIAN/control, package murasaki-common, directory debian/murasaki-common pkgstripfiles: Running PNG optimization (using 4 cpus) for package murasaki-common ... pkgstripfiles: No PNG files. dpkg-deb: building package 'murasaki-common' in '../murasaki-common_1.68.6-6build2_all.deb'. dpkg-genchanges --build=any,all -mLaunchpad Build Daemon >../murasaki_1.68.6-6build2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build murasaki-1.68.6 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20161022-0149 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ murasaki_1.68.6-6build2_amd64.changes: -------------------------------------- Format: 1.8 Date: Sat, 22 Oct 2016 01:39:57 +0000 Source: murasaki Binary: murasaki murasaki-mpi murasaki-common Architecture: all amd64 Version: 1.68.6-6build2 Distribution: zesty-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steve Langasek Description: murasaki - homology detection tool across multiple large genomes murasaki-common - homology detection tool across multiple large genomes (common fil murasaki-mpi - homology detection tool across multiple large genomes (MPI-versio Changes: murasaki (1.68.6-6build2) zesty; urgency=medium . * No-change rebuild against libopenmpi2 Checksums-Sha1: d676184d885551b16f3ba78a2c50f157d0a5e186 143940 murasaki-common_1.68.6-6build2_all.deb b14b558c3dab1a7ff4968bab663069bb8d48b0ec 6009796 murasaki-dbgsym_1.68.6-6build2_amd64.ddeb 92e2a5731df423df318800006e9f4020459ea961 6998580 murasaki-mpi-dbgsym_1.68.6-6build2_amd64.ddeb 5d36bb7dbb7e7b3edd7e14a46360cc632866ee5c 596726 murasaki-mpi_1.68.6-6build2_amd64.deb 44e17ff83005a84adfeef55412dc6194f4c22ef2 492080 murasaki_1.68.6-6build2_amd64.deb Checksums-Sha256: cd85f5f1006bbf697af6b74c01721c0b27d11f321f455bd3c4c166bb022c9da6 143940 murasaki-common_1.68.6-6build2_all.deb 1960a9adb6a2981938f012780cd44fad8cd7674c51d4200a78f25bddebafe5e9 6009796 murasaki-dbgsym_1.68.6-6build2_amd64.ddeb 1eb0eddac14e3b55b14a01cbefbc7aab36e63989f296238f5c917a6766372b20 6998580 murasaki-mpi-dbgsym_1.68.6-6build2_amd64.ddeb 34d6ad45bca6debbcaab6dda95604d1d4768cd849d7162802903ef5ca5119d7b 596726 murasaki-mpi_1.68.6-6build2_amd64.deb 0c93d0bcc0d532ceabf8210917b726b20e50a2677f590796f1e3cdedacc2b802 492080 murasaki_1.68.6-6build2_amd64.deb Files: 1830f5c46bdf95ebf49d6904759d0425 143940 science optional murasaki-common_1.68.6-6build2_all.deb ebd87c4259797c825dc2dc4677fd4a1e 6009796 science extra murasaki-dbgsym_1.68.6-6build2_amd64.ddeb 36185c91bcd22f6118b4b331b3d9de13 6998580 science extra murasaki-mpi-dbgsym_1.68.6-6build2_amd64.ddeb bd2ef25e3d5801a53f824ceb1152224e 596726 science optional murasaki-mpi_1.68.6-6build2_amd64.deb 5fed6a2dd21ea0261c3d4b625991be65 492080 science optional murasaki_1.68.6-6build2_amd64.deb Original-Maintainer: Debian Med Packaging Team +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ murasaki-common_1.68.6-6build2_all.deb -------------------------------------- new debian package, version 2.0. size 143940 bytes: control archive=3360 bytes. 1366 bytes, 29 lines control 6107 bytes, 84 lines md5sums Package: murasaki-common Source: murasaki Version: 1.68.6-6build2 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 429 Depends: gnuplot | gnuplot5, libbio-perl-perl, r-cran-rocr, imagemagick Recommends: libterm-readkey-perl, libtext-wrapi18n-perl | libtext-wrapper-perl Section: science Priority: optional Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Description: homology detection tool across multiple large genomes (common files) Murasaki is a scalable and fast, language theory-based homology detection tool across multiple large genomes. It enable whole-genome scale multiple genome global alignments. Supports unlimited length gapped-seed patterns and unique TF-IDF based filtering. . Murasaki is an anchor alignment software, which is * exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 52 wall minutes)) * scalable (Arbitrarily parallelizable across multiple nodes using MPI. Even a single node with 16GB of ram can handle over 1Gbp of sequence.) * unlimited pattern length * repeat tolerant * intelligent noise reduction . This package contains all files that are common to the single core murasaki package and the multi core murasaki-mpi package. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2016-10-22 01:39 ./ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/lib/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/lib/debian-med/bin/ -rwxr-xr-x root/root 3948 2010-08-24 14:18 ./usr/lib/debian-med/bin/align2kog.pl -rwxr-xr-x root/root 5024 2010-08-24 14:18 ./usr/lib/debian-med/bin/analyze-pat.pl -rwxr-xr-x root/root 3917 2010-08-24 14:18 ./usr/lib/debian-med/bin/anchors2maf.pl -rwxr-xr-x root/root 5334 2010-08-24 14:18 ./usr/lib/debian-med/bin/anchors2osfinder.pl -rwxr-xr-x root/root 1973 2010-08-24 14:18 ./usr/lib/debian-med/bin/antisense.pl -rwxr-xr-x root/root 4401 2010-08-24 14:18 ./usr/lib/debian-med/bin/chromostitch.pl -rwxr-xr-x root/root 2745 2010-08-24 14:18 ./usr/lib/debian-med/bin/dna2binary.pl -rwxr-xr-x root/root 1939 2010-08-24 14:18 ./usr/lib/debian-med/bin/dnashuffle.pl -rwxr-xr-x root/root 2331 2010-08-24 14:18 ./usr/lib/debian-med/bin/faformat.pl -rwxr-xr-x root/root 55969 2016-10-22 01:39 ./usr/lib/debian-med/bin/filter.pl -rwxr-xr-x root/root 7335 2010-08-24 14:18 ./usr/lib/debian-med/bin/gatherstats.pl -rwxr-xr-x root/root 8380 2010-08-24 14:18 ./usr/lib/debian-med/bin/geneparse.pl -rwxr-xr-x root/root 21536 2010-08-24 14:18 ./usr/lib/debian-med/bin/getcds.pl -rwxr-xr-x root/root 3644 2010-08-24 14:18 ./usr/lib/debian-med/bin/getgene.pl -rwxr-xr-x root/root 5458 2010-08-24 14:18 ./usr/lib/debian-med/bin/histocomp.pl -rwxr-xr-x root/root 4341 2010-08-24 14:18 ./usr/lib/debian-med/bin/histoplot.pl -rwxr-xr-x root/root 7097 2010-08-24 14:18 ./usr/lib/debian-med/bin/homology-score.pl -rwxr-xr-x root/root 898 2010-08-24 14:18 ./usr/lib/debian-med/bin/humantime.pl -rwxr-xr-x root/root 4675 2010-08-24 14:18 ./usr/lib/debian-med/bin/interpolate.pl -rwxr-xr-x root/root 6016 2010-08-24 14:18 ./usr/lib/debian-med/bin/kogalign.pl -rwxr-xr-x root/root 5770 2010-08-24 14:18 ./usr/lib/debian-med/bin/lav2murasaki.pl -rwxr-xr-x root/root 8150 2010-08-24 14:18 ./usr/lib/debian-med/bin/maf2anchors.pl -rwxr-xr-x root/root 4012 2010-08-24 14:18 ./usr/lib/debian-med/bin/mauve2anchors.pl -rwxr-xr-x root/root 5185 2010-08-24 14:18 ./usr/lib/debian-med/bin/mauveAlignment2anchors.pl -rwxr-xr-x root/root 2931 2010-08-24 14:18 ./usr/lib/debian-med/bin/mbgd-to-kog.pl -rwxr-xr-x root/root 1473 2010-08-24 14:18 ./usr/lib/debian-med/bin/mfasplit.pl -rwxr-xr-x root/root 3708 2010-08-24 14:18 ./usr/lib/debian-med/bin/names2kog.pl -rwxr-xr-x root/root 4090 2010-08-24 14:18 ./usr/lib/debian-med/bin/osfinder2anchors.pl -rwxr-xr-x root/root 2734 2010-08-24 14:18 ./usr/lib/debian-med/bin/overlay.pl -rwxr-xr-x root/root 3765 2010-08-24 14:18 ./usr/lib/debian-med/bin/phAlignment2anchors.pl -rwxr-xr-x root/root 6152 2016-10-22 01:39 ./usr/lib/debian-med/bin/qlob.pl -rwxr-xr-x root/root 1952 2010-08-24 14:18 ./usr/lib/debian-med/bin/randpat.pl -rwxr-xr-x root/root 3051 2010-08-24 14:18 ./usr/lib/debian-med/bin/rearrange.pl -rwxr-xr-x root/root 2794 2010-08-24 14:18 ./usr/lib/debian-med/bin/repeats2anchors.pl -rwxr-xr-x root/root 10809 2010-08-24 14:18 ./usr/lib/debian-med/bin/repeatviz.pl -rwxr-xr-x root/root 9502 2010-08-24 14:18 ./usr/lib/debian-med/bin/roc-at-cutoff.pl -rwxr-xr-x root/root 6378 2010-08-24 14:18 ./usr/lib/debian-med/bin/simpal.pl -rwxr-xr-x root/root 13783 2010-08-24 14:18 ./usr/lib/debian-med/bin/simplegraph.pl -rwxr-xr-x root/root 6884 2010-08-24 14:18 ./usr/lib/debian-med/bin/stat-histo.pl -rwxr-xr-x root/root 6875 2010-08-24 14:18 ./usr/lib/debian-med/bin/stat-vs-stat.pl -rwxr-xr-x root/root 14985 2016-10-22 01:39 ./usr/lib/debian-med/bin/substitch.pl drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/doc/murasaki-common/ -rw-r--r-- root/root 238 2016-07-12 07:25 ./usr/share/doc/murasaki-common/README.Debian -rw-r--r-- root/root 840 2016-10-22 01:39 ./usr/share/doc/murasaki-common/changelog.Debian.gz -rw-r--r-- root/root 2221 2016-07-12 07:25 ./usr/share/doc/murasaki-common/copyright drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/man/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/man/man1/ -rw-r--r-- root/root 1968 2016-10-22 01:39 ./usr/share/man/man1/align2kog.pl.1.gz -rw-r--r-- root/root 1948 2016-10-22 01:39 ./usr/share/man/man1/analyze-pat.pl.1.gz -rw-r--r-- root/root 2196 2016-10-22 01:39 ./usr/share/man/man1/chromostitch.pl.1.gz -rw-r--r-- root/root 2030 2016-10-22 01:39 ./usr/share/man/man1/faformat.pl.1.gz -rw-r--r-- root/root 4047 2016-10-22 01:39 ./usr/share/man/man1/filter.pl.1.gz -rw-r--r-- root/root 2020 2016-10-22 01:39 ./usr/share/man/man1/gatherstats.pl.1.gz -rw-r--r-- root/root 2723 2016-10-22 01:39 ./usr/share/man/man1/getcds.pl.1.gz -rw-r--r-- root/root 1967 2016-10-22 01:39 ./usr/share/man/man1/getgene.pl.1.gz -rw-r--r-- root/root 2022 2016-10-22 01:39 ./usr/share/man/man1/histocomp.pl.1.gz -rw-r--r-- root/root 2419 2016-10-22 01:39 ./usr/share/man/man1/histoplot.pl.1.gz -rw-r--r-- root/root 2020 2016-10-22 01:39 ./usr/share/man/man1/homology-score.pl.1.gz -rw-r--r-- root/root 1984 2016-10-22 01:39 ./usr/share/man/man1/interpolate.pl.1.gz -rw-r--r-- root/root 1946 2016-10-22 01:39 ./usr/share/man/man1/kogalign.pl.1.gz -rw-r--r-- root/root 2139 2016-10-22 01:39 ./usr/share/man/man1/lav2murasaki.pl.1.gz -rw-r--r-- root/root 2287 2016-10-22 01:39 ./usr/share/man/man1/maf2anchors.pl.1.gz -rw-r--r-- root/root 1921 2016-10-22 01:39 ./usr/share/man/man1/mauve2anchors.pl.1.gz -rw-r--r-- root/root 2037 2016-10-22 01:39 ./usr/share/man/man1/mauveAlignment2anchors.pl.1.gz -rw-r--r-- root/root 1943 2016-10-22 01:39 ./usr/share/man/man1/mbgd-to-kog.pl.1.gz -rw-r--r-- root/root 1871 2016-10-22 01:39 ./usr/share/man/man1/mfasplit.pl.1.gz -rw-r--r-- root/root 2063 2016-10-22 01:39 ./usr/share/man/man1/names2kog.pl.1.gz -rw-r--r-- root/root 2149 2016-10-22 01:39 ./usr/share/man/man1/overlay.pl.1.gz -rw-r--r-- root/root 1914 2016-10-22 01:39 ./usr/share/man/man1/phAlignment2anchors.pl.1.gz -rw-r--r-- root/root 2329 2016-10-22 01:39 ./usr/share/man/man1/qlob.pl.1.gz -rw-r--r-- root/root 1945 2016-10-22 01:39 ./usr/share/man/man1/rearrange.pl.1.gz -rw-r--r-- root/root 1896 2016-10-22 01:39 ./usr/share/man/man1/repeats2anchors.pl.1.gz -rw-r--r-- root/root 2524 2016-10-22 01:39 ./usr/share/man/man1/repeatviz.pl.1.gz -rw-r--r-- root/root 2410 2016-10-22 01:39 ./usr/share/man/man1/roc-at-cutoff.pl.1.gz -rw-r--r-- root/root 2076 2016-10-22 01:39 ./usr/share/man/man1/simpal.pl.1.gz -rw-r--r-- root/root 2338 2016-10-22 01:39 ./usr/share/man/man1/simplegraph.pl.1.gz -rw-r--r-- root/root 2293 2016-10-22 01:39 ./usr/share/man/man1/stat-histo.pl.1.gz -rw-r--r-- root/root 2393 2016-10-22 01:39 ./usr/share/man/man1/stat-vs-stat.pl.1.gz -rw-r--r-- root/root 2443 2016-10-22 01:39 ./usr/share/man/man1/substitch.pl.1.gz drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/perl5/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/perl5/murasaki/ -rw-r--r-- root/root 3047 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki.pm drwxr-xr-x root/root 0 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki/ -rw-r--r-- root/root 8037 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki/KOG.pm -rw-r--r-- root/root 7146 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki/OrthoConsistency.pm -rw-r--r-- root/root 4383 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki/OrthoList.pm -rw-r--r-- root/root 8019 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki/OrthoPairs.pm -rw-r--r-- root/root 2893 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki/SeqFeatures.pm -rw-r--r-- root/root 1459 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki/Ticker.pm -rwxr-xr-x root/root 137 2016-07-12 07:25 ./usr/share/perl5/murasaki/config.pl murasaki-mpi_1.68.6-6build2_amd64.deb ------------------------------------- new debian package, version 2.0. size 596726 bytes: control archive=1501 bytes. 1448 bytes, 29 lines control 1116 bytes, 17 lines md5sums Package: murasaki-mpi Source: murasaki Version: 1.68.6-6build2 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 3939 Depends: murasaki-common, libboost-filesystem1.61.0, libboost-iostreams1.61.0, libboost-regex1.61.0, libboost-system1.61.0, libc6 (>= 2.14), libgcc1 (>= 1:3.0), libopenmpi2, libstdc++6 (>= 5.2) Section: science Priority: optional Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Description: homology detection tool across multiple large genomes (MPI-version) Murasaki is a scalable and fast, language theory-based homology detection tool across multiple large genomes. It enable whole-genome scale multiple genome global alignments. Supports unlimited length gapped-seed patterns and unique TF-IDF based filtering. . Murasaki is an anchor alignment software, which is * exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 52 wall minutes)) * scalable (Arbitrarily parallelizable across multiple nodes using MPI. Even a single node with 16GB of ram can handle over 1Gbp of sequence.) * unlimited pattern length * repeat tolerant * intelligent noise reduction . This package provides the MPI-enabled binary for murasaki. While this will speed up operation on multi-processor machines it will slow down on a single processor. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2016-10-22 01:39 ./ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/bin/ -rwxr-xr-x root/root 252496 2016-10-22 01:39 ./usr/bin/geneparse-mpi -rwxr-xr-x root/root 362968 2016-10-22 01:39 ./usr/bin/mbfa-mpi -rwxr-xr-x root/root 807640 2016-10-22 01:39 ./usr/bin/murasaki-mpi drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/lib/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/lib/murasaki/ -rwxr-xr-x root/root 252280 2016-10-22 01:39 ./usr/lib/murasaki/align-and-mpi -rwxr-xr-x root/root 260504 2016-10-22 01:39 ./usr/lib/murasaki/align-best-mpi -rwxr-xr-x root/root 281024 2016-10-22 01:39 ./usr/lib/murasaki/align-compare-mpi -rwxr-xr-x root/root 379352 2016-10-22 01:39 ./usr/lib/murasaki/align-coverage-mpi -rwxr-xr-x root/root 248152 2016-10-22 01:39 ./usr/lib/murasaki/align-or-mpi -rwxr-xr-x root/root 166216 2016-10-22 01:39 ./usr/lib/murasaki/cgr-compare-mpi -rwxr-xr-x root/root 379448 2016-10-22 01:39 ./usr/lib/murasaki/cgr-image-mpi -rwxr-xr-x root/root 7138 2010-08-24 14:18 ./usr/lib/murasaki/cgr-image.pl-mpi -rwxr-xr-x root/root 170352 2016-10-22 01:39 ./usr/lib/murasaki/cgr-random-mpi -rwxr-xr-x root/root 301584 2016-10-22 01:39 ./usr/lib/murasaki/cgr-sample-mpi -rwxr-xr-x root/root 137384 2016-10-22 01:39 ./usr/lib/murasaki/testeco-mpi drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/doc/murasaki-mpi/ -rw-r--r-- root/root 249 2016-07-12 07:25 ./usr/share/doc/murasaki-mpi/README.test -rw-r--r-- root/root 840 2016-10-22 01:39 ./usr/share/doc/murasaki-mpi/changelog.Debian.gz -rw-r--r-- root/root 2221 2016-07-12 07:25 ./usr/share/doc/murasaki-mpi/copyright drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/man/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/man/man1/ lrwxrwxrwx root/root 0 2016-10-22 01:39 ./usr/share/man/man1/geneparse-mpi.1.gz -> geneparse.1.gz lrwxrwxrwx root/root 0 2016-10-22 01:39 ./usr/share/man/man1/mbfa-mpi.1.gz -> mbfa.1.gz lrwxrwxrwx root/root 0 2016-10-22 01:39 ./usr/share/man/man1/murasaki-mpi.1.gz -> murasaki.1.gz murasaki_1.68.6-6build2_amd64.deb --------------------------------- new debian package, version 2.0. size 492080 bytes: control archive=1436 bytes. 1230 bytes, 24 lines control 1182 bytes, 19 lines md5sums Package: murasaki Version: 1.68.6-6build2 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 3102 Depends: murasaki-common, libboost-filesystem1.61.0, libboost-iostreams1.61.0, libboost-regex1.61.0, libboost-system1.61.0, libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2) Section: science Priority: optional Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Description: homology detection tool across multiple large genomes Murasaki is a scalable and fast, language theory-based homology detection tool across multiple large genomes. It enable whole-genome scale multiple genome global alignments. Supports unlimited length gapped-seed patterns and unique TF-IDF based filtering. . Murasaki is an anchor alignment software, which is * exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 52 wall minutes)) * scalable (Arbitrarily parallelizable across multiple nodes using MPI. Even a single node with 16GB of ram can handle over 1Gbp of sequence.) * unlimited pattern length * repeat tolerant * intelligent noise reduction Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2016-10-22 01:39 ./ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/bin/ -rwxr-xr-x root/root 252496 2016-10-22 01:39 ./usr/bin/geneparse -rwxr-xr-x root/root 293336 2016-10-22 01:39 ./usr/bin/mbfa -rwxr-xr-x root/root 635576 2016-10-22 01:39 ./usr/bin/murasaki drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/lib/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/lib/murasaki/ -rwxr-xr-x root/root 182648 2016-10-22 01:39 ./usr/lib/murasaki/align-and -rwxr-xr-x root/root 190872 2016-10-22 01:39 ./usr/lib/murasaki/align-best -rwxr-xr-x root/root 211392 2016-10-22 01:39 ./usr/lib/murasaki/align-compare -rwxr-xr-x root/root 309720 2016-10-22 01:39 ./usr/lib/murasaki/align-coverage -rwxr-xr-x root/root 182616 2016-10-22 01:39 ./usr/lib/murasaki/align-or -rwxr-xr-x root/root 96584 2016-10-22 01:39 ./usr/lib/murasaki/cgr-compare -rwxr-xr-x root/root 309816 2016-10-22 01:39 ./usr/lib/murasaki/cgr-image -rwxr-xr-x root/root 100720 2016-10-22 01:39 ./usr/lib/murasaki/cgr-random -rwxr-xr-x root/root 301584 2016-10-22 01:39 ./usr/lib/murasaki/cgr-sample -rwxr-xr-x root/root 67752 2016-10-22 01:39 ./usr/lib/murasaki/testeco drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/doc/murasaki/ -rw-r--r-- root/root 249 2016-07-12 07:25 ./usr/share/doc/murasaki/README.test -rw-r--r-- root/root 840 2016-10-22 01:39 ./usr/share/doc/murasaki/changelog.Debian.gz -rw-r--r-- root/root 2221 2016-07-12 07:25 ./usr/share/doc/murasaki/copyright drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/man/ drwxr-xr-x root/root 0 2016-10-22 01:39 ./usr/share/man/man1/ -rw-r--r-- root/root 2518 2016-10-22 01:39 ./usr/share/man/man1/geneparse.1.gz -rw-r--r-- root/root 2721 2016-10-22 01:39 ./usr/share/man/man1/mbfa.1.gz -rw-r--r-- root/root 10888 2016-10-22 01:39 ./usr/share/man/man1/murasaki.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 161068 Build-Time: 459 Distribution: zesty-proposed Host Architecture: amd64 Install-Time: 34 Job: murasaki_1.68.6-6build2.dsc Machine Architecture: amd64 Package: murasaki Package-Time: 495 Source-Version: 1.68.6-6build2 Space: 161068 Status: successful Version: 1.68.6-6build2 -------------------------------------------------------------------------------- Finished at 20161022-0149 Build needed 00:08:15, 161068k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-11057403'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-11057403/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-11057403'] Unmounting chroot for build PACKAGEBUILD-11057403... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-11057403'] Removing build PACKAGEBUILD-11057403