https://launchpad.net/ubuntu/+source/anfo/0.98-7/+build/15625131 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lcy01-amd64-017 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 UTC 2018 x86_64 Buildd toolchain package versions: launchpad-buildd_165 python-lpbuildd_165 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.5 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 9 Nov 07:20:47 ntpdate[1816]: adjust time server 10.211.37.1 offset 0.000510 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15625131 /home/buildd/filecache-default/b71572c9405b6ce6ff1d1ad001cf764bb07f52ae Creating target for build PACKAGEBUILD-15625131 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15625131 Starting target for build PACKAGEBUILD-15625131 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15625131 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15625131 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15625131 Updating target for build PACKAGEBUILD-15625131 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main amd64 Packages [1018 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [513 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe amd64 Packages [8779 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5053 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 Packages [44.3 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [25.7 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 Packages [113 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [65.8 kB] Fetched 16.1 MB in 4s (3972 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libgdbm6 libperl5.28 perl-modules-5.28 The following packages will be upgraded: base-files binutils binutils-common binutils-x86-64-linux-gnu cpp cpp-8 dash dmsetup g++ g++-8 gcc gcc-8 gcc-8-base libapparmor1 libasan5 libatomic1 libaudit-common libaudit1 libbinutils libcap-ng0 libcc1-0 libdevmapper1.02.1 libgcc-8-dev libgcc1 libgdbm-compat4 libgomp1 libitm1 libkmod2 liblsan0 libmpx2 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libstdc++-8-dev libstdc++6 libsystemd0 libtsan0 libubsan1 libudev1 linux-libc-dev perl perl-base systemd systemd-sysv tzdata 47 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 44.9 MB of archives. After this operation, 48.6 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main amd64 base-files amd64 10.1ubuntu8 [60.1 kB] Get:2 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 dash amd64 0.5.10.2-1 [89.3 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main amd64 perl-modules-5.28 all 5.28.0-3 [2818 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main amd64 libgdbm6 amd64 1.18.1-1 [27.8 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main amd64 libgdbm-compat4 amd64 1.18.1-1 [6148 B] Get:6 http://ftpmaster.internal/ubuntu disco/main amd64 libperl5.28 amd64 5.28.0-3 [3804 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main amd64 perl amd64 5.28.0-3 [204 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main amd64 perl-base amd64 5.28.0-3 [1510 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 systemd-sysv amd64 239-7ubuntu10.1 [9404 B] Get:10 http://ftpmaster.internal/ubuntu disco/main amd64 libapparmor1 amd64 2.12-4ubuntu10 [29.9 kB] Get:11 http://ftpmaster.internal/ubuntu disco/main amd64 libaudit-common all 1:2.8.3-1ubuntu3 [4068 B] Get:12 http://ftpmaster.internal/ubuntu disco/main amd64 libcap-ng0 amd64 0.7.9-1build1 [10.9 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main amd64 libaudit1 amd64 1:2.8.3-1ubuntu3 [38.8 kB] Get:14 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libkmod2 amd64 25-1ubuntu1.1 [41.8 kB] Get:15 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 systemd amd64 239-7ubuntu10.1 [2968 kB] Get:16 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libsystemd0 amd64 239-7ubuntu10.1 [211 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main amd64 libquadmath0 amd64 8.2.0-9ubuntu1 [134 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main amd64 libubsan1 amd64 8.2.0-9ubuntu1 [121 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main amd64 libitm1 amd64 8.2.0-9ubuntu1 [28.1 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main amd64 libasan5 amd64 8.2.0-9ubuntu1 [364 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main amd64 gcc-8-base amd64 8.2.0-9ubuntu1 [18.6 kB] Get:22 http://ftpmaster.internal/ubuntu disco/main amd64 libstdc++6 amd64 8.2.0-9ubuntu1 [399 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main amd64 libgomp1 amd64 8.2.0-9ubuntu1 [76.4 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main amd64 libatomic1 amd64 8.2.0-9ubuntu1 [9076 B] Get:25 http://ftpmaster.internal/ubuntu disco/main amd64 liblsan0 amd64 8.2.0-9ubuntu1 [132 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main amd64 libtsan0 amd64 8.2.0-9ubuntu1 [288 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main amd64 libmpx2 amd64 8.2.0-9ubuntu1 [11.7 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main amd64 cpp-8 amd64 8.2.0-9ubuntu1 [7222 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main amd64 libcc1-0 amd64 8.2.0-9ubuntu1 [39.5 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main amd64 gcc-8 amd64 8.2.0-9ubuntu1 [7999 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main amd64 g++-8 amd64 8.2.0-9ubuntu1 [8115 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main amd64 libstdc++-8-dev amd64 8.2.0-9ubuntu1 [1538 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main amd64 libgcc-8-dev amd64 8.2.0-9ubuntu1 [2304 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main amd64 libgcc1 amd64 1:8.2.0-9ubuntu1 [40.7 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main amd64 libbinutils amd64 2.31.1-7ubuntu1 [483 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main amd64 binutils-common amd64 2.31.1-7ubuntu1 [194 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main amd64 binutils amd64 2.31.1-7ubuntu1 [3392 B] Get:38 http://ftpmaster.internal/ubuntu disco/main amd64 binutils-x86-64-linux-gnu amd64 2.31.1-7ubuntu1 [1829 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main amd64 libselinux1 amd64 2.8-1build2 [68.6 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main amd64 libsemanage-common all 2.8-1build2 [6892 B] Get:41 http://ftpmaster.internal/ubuntu disco/main amd64 libsemanage1 amd64 2.8-1build2 [85.1 kB] Get:42 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libudev1 amd64 239-7ubuntu10.1 [53.9 kB] Get:43 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libseccomp2 amd64 2.3.3-3ubuntu2 [38.9 kB] Get:44 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libdevmapper1.02.1 amd64 2:1.02.145-4.1ubuntu4 [127 kB] Get:45 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 dmsetup amd64 2:1.02.145-4.1ubuntu4 [74.6 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main amd64 tzdata all 2018g-1 [188 kB] Get:47 http://ftpmaster.internal/ubuntu disco/main amd64 g++ amd64 4:8.2.0-2ubuntu2 [1608 B] Get:48 http://ftpmaster.internal/ubuntu disco/main amd64 gcc amd64 4:8.2.0-2ubuntu2 [5224 B] Get:49 http://ftpmaster.internal/ubuntu disco/main amd64 cpp amd64 4:8.2.0-2ubuntu2 [27.6 kB] Get:50 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 linux-libc-dev amd64 4.18.0-11.12 [1039 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 44.9 MB in 1s (44.0 MB/s) (Reading database ... 12650 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu8_amd64.deb ... Unpacking base-files (10.1ubuntu8) over (10.1ubuntu7) ... Setting up base-files (10.1ubuntu8) ... 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 ... 12650 files and directories currently installed.) Preparing to unpack .../dash_0.5.10.2-1_amd64.deb ... Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' Unpacking dash (0.5.10.2-1) over (0.5.8-2.10) ... Setting up dash (0.5.10.2-1) ... Removing 'diversion of /bin/sh to /bin/sh.distrib by bash' Adding 'diversion of /bin/sh to /bin/sh.distrib by dash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' (Reading database ... 12650 files and directories currently installed.) Preparing to unpack .../0-perl_5.28.0-3_amd64.deb ... Unpacking perl (5.28.0-3) over (5.26.2-7) ... Selecting previously unselected package perl-modules-5.28. Preparing to unpack .../1-perl-modules-5.28_5.28.0-3_all.deb ... Unpacking perl-modules-5.28 (5.28.0-3) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../2-libgdbm6_1.18.1-1_amd64.deb ... Unpacking libgdbm6:amd64 (1.18.1-1) ... Preparing to unpack .../3-libgdbm-compat4_1.18.1-1_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.18.1-1) over (1.14.1-6) ... Selecting previously unselected package libperl5.28:amd64. 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Universal Time is now: Fri Nov 9 07:21:09 UTC 2018. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libtsan0:amd64 (8.2.0-9ubuntu1) ... Setting up linux-libc-dev:amd64 (4.18.0-11.12) ... Setting up libdevmapper1.02.1:amd64 (2:1.02.145-4.1ubuntu4) ... Setting up libkmod2:amd64 (25-1ubuntu1.1) ... Setting up liblsan0:amd64 (8.2.0-9ubuntu1) ... Setting up libgdbm6:amd64 (1.18.1-1) ... Setting up binutils-common:amd64 (2.31.1-7ubuntu1) ... Setting up libmpx2:amd64 (8.2.0-9ubuntu1) ... Setting up perl-modules-5.28 (5.28.0-3) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up libapparmor1:amd64 (2.12-4ubuntu10) ... Setting up systemd (239-7ubuntu10.1) ... Setting up dmsetup (2:1.02.145-4.1ubuntu4) ... Setting up libgdbm-compat4:amd64 (1.18.1-1) ... Setting up libasan5:amd64 (8.2.0-9ubuntu1) ... Setting up libitm1:amd64 (8.2.0-9ubuntu1) ... Setting up libubsan1:amd64 (8.2.0-9ubuntu1) ... Setting up libbinutils:amd64 (2.31.1-7ubuntu1) ... Setting up libperl5.28:amd64 (5.28.0-3) ... Setting up systemd-sysv (239-7ubuntu10.1) ... Setting up perl (5.28.0-3) ... Setting up libgcc-8-dev:amd64 (8.2.0-9ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.31.1-7ubuntu1) ... Setting up libstdc++-8-dev:amd64 (8.2.0-9ubuntu1) ... Setting up binutils (2.31.1-7ubuntu1) ... Setting up gcc-8 (8.2.0-9ubuntu1) ... Setting up g++-8 (8.2.0-9ubuntu1) ... Setting up gcc (4:8.2.0-2ubuntu2) ... Setting up g++ (4:8.2.0-2ubuntu2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15625131 amd64 disco-proposed -c chroot:build-PACKAGEBUILD-15625131 --arch=amd64 --dist=disco-proposed --nolog -A anfo_0.98-7.dsc Initiating build PACKAGEBUILD-15625131 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 UTC 2018 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-017.buildd +==============================================================================+ | anfo 0.98-7 (amd64) 09 Nov 2018 07:21 | +==============================================================================+ Package: anfo Version: 0.98-7 Source Version: 0.98-7 Distribution: disco-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/anfo-gNS8JA/anfo-0.98' with '<>' I: NOTICE: Log filtering will replace 'build/anfo-gNS8JA' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15625131/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- anfo_0.98-7.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-wr6J5r/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-wr6J5r/apt_archive ./ InRelease Get:2 copy:/<>/resolver-wr6J5r/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-wr6J5r/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-wr6J5r/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-wr6J5r/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (213 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-wr6J5r/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14539 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 (>= 11~), libpopt-dev, libprotobuf-dev, libelk0-dev, libelk0, zlib1g-dev, libbz2-dev, pkg-config, protobuf-compiler, d-shlibs (>= 0.77) Filtered Build-Depends: debhelper (>= 11~), libpopt-dev, libprotobuf-dev, libelk0-dev, libelk0, zlib1g-dev, libbz2-dev, pkg-config, protobuf-compiler, d-shlibs (>= 0.77) dpkg-deb: building package 'sbuild-build-depends-anfo-dummy' in '/<>/resolver-4rfCWc/apt_archive/sbuild-build-depends-anfo-dummy.deb'. Ign:1 copy:/<>/resolver-4rfCWc/apt_archive ./ InRelease Get:2 copy:/<>/resolver-4rfCWc/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-4rfCWc/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-4rfCWc/apt_archive ./ Sources [273 B] Get:5 copy:/<>/resolver-4rfCWc/apt_archive ./ Packages [589 B] Fetched 2981 B in 0s (230 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install anfo build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3 libelf-dev libelf1 libelk0 libelk0-dev libfile-stripnondeterminism-perl libglib2.0-0 libice-dev libice6 libicu60 libmagic-mgc libmagic1 libpipeline1 libpopt-dev libpopt0 libprotobuf-dev libprotobuf-lite10 libprotobuf10 libprotoc10 libpthread-stubs0-dev libsigsegv2 libsm-dev libsm6 libtimedate-perl libtool libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxml2 libxmu-dev libxmu-headers libxmu6 libxt-dev libxt6 m4 man-db pkg-config po-debconf protobuf-compiler x11-common x11proto-core-dev x11proto-dev x11proto-xext-dev xorg-sgml-doctools xtrans-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libice-doc libsm-doc libtool-doc gfortran | fortran95-compiler gcj-jdk libx11-doc libxcb-doc libxext-doc libxt-doc m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3 libelf-dev libelf1 libelk0 libelk0-dev libfile-stripnondeterminism-perl libglib2.0-0 libice-dev libice6 libicu60 libmagic-mgc libmagic1 libpipeline1 libpopt-dev libpopt0 libprotobuf-dev libprotobuf-lite10 libprotobuf10 libprotoc10 libpthread-stubs0-dev libsigsegv2 libsm-dev libsm6 libtimedate-perl libtool libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxml2 libxmu-dev libxmu-headers libxmu6 libxt-dev libxt6 m4 man-db pkg-config po-debconf protobuf-compiler sbuild-build-depends-anfo-dummy x11-common x11proto-core-dev x11proto-dev x11proto-xext-dev xorg-sgml-doctools xtrans-dev zlib1g-dev 0 upgraded, 73 newly installed, 0 to remove and 0 not upgraded. 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Processing triggers for systemd (239-7ubuntu10.1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-138-generic amd64 (x86_64) Toolchain package versions: binutils_2.31.1-7ubuntu1 dpkg-dev_1.19.0.5ubuntu5 g++-8_8.2.0-9ubuntu1 gcc-8_8.2.0-9ubuntu1 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-9ubuntu1 libstdc++6_8.2.0-9ubuntu1 linux-libc-dev_4.18.0-11.12 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.7.0 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-8 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_4.4.18-2ubuntu3 binutils_2.31.1-7ubuntu1 binutils-common_2.31.1-7ubuntu1 binutils-x86-64-linux-gnu_2.31.1-7ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu2 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20180409 coreutils_8.28-1ubuntu2 cpp_4:8.2.0-2ubuntu2 cpp-8_8.2.0-9ubuntu1 d-shlibs_0.82+nmu1 dash_0.5.10.2-1 debconf_1.5.69 debhelper_11.3.2ubuntu1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu4 dpkg_1.19.0.5ubuntu5 dpkg-dev_1.19.0.5ubuntu5 dwz_0.12-2 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 fakeroot_1.22-2ubuntu1 fdisk_2.32-0.1ubuntu2 file_1:5.34-2 findutils_4.6.0+git+20180808-2 g++_4:8.2.0-2ubuntu2 g++-8_8.2.0-9ubuntu1 gcc_4:8.2.0-2ubuntu2 gcc-8_8.2.0-9ubuntu1 gcc-8-base_8.2.0-9ubuntu1 gettext_0.19.8.1-8 gettext-base_0.19.8.1-8 gpg_2.2.8-3ubuntu1 gpg-agent_2.2.8-3ubuntu1 gpgconf_2.2.8-3ubuntu1 gpgv_2.2.8-3ubuntu1 grep_3.1-2ubuntu1 groff-base_1.22.3-10 gzip_1.6-5ubuntu2 hostname_3.20 init_1.54 init-system-helpers_1.54 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu10 libapt-pkg5.0_1.7.0 libarchive-zip-perl_1.63-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-9ubuntu1 libassuan0_2.5.1-2 libatomic1_8.2.0-9ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu3 libaudit1_1:2.8.3-1ubuntu3 libbinutils_2.31.1-7ubuntu1 libblkid1_2.32-0.1ubuntu2 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libbz2-dev_1.0.6-9 libc-bin_2.28-0ubuntu1 libc-dev-bin_2.28-0ubuntu1 libc6_2.28-0ubuntu1 libc6-dev_2.28-0ubuntu1 libcap-ng0_0.7.9-1build1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-9ubuntu1 libcom-err2_1.44.4-2 libcomerr2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2ubuntu2 libdb5.3_5.3.28+dfsg1-0.1 libdebconfclient0_0.244ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu4 libdpkg-perl_1.19.0.5ubuntu5 libelf-dev_0.170-0.5.0ubuntu1 libelf1_0.170-0.5.0ubuntu1 libelk0_3.99.8-4.2 libelk0-dev_3.99.8-4.2 libext2fs2_1.44.4-2 libfakeroot_1.22-2ubuntu1 libfdisk1_2.32-0.1ubuntu2 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libgcc-8-dev_8.2.0-9ubuntu1 libgcc1_1:8.2.0-9ubuntu1 libgcrypt20_1.8.3-1ubuntu1 libgdbm-compat4_1.18.1-1 libgdbm5_1.14.1-6 libgdbm6_1.18.1-1 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.6.4-2ubuntu1 libgomp1_8.2.0-9ubuntu1 libgpg-error0_1.32-1 libhogweed4_3.4-1 libice-dev_2:1.0.9-2 libice6_2:1.0.9-2 libicu60_60.2-6ubuntu1 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.5-1 libip4tc0_1.6.1-2ubuntu2 libisl19_0.20-2 libitm1_8.2.0-9ubuntu1 libjson-c3_0.12.1-1.3 libkmod2_25-1ubuntu1.1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_8.2.0-9ubuntu1 liblz4-1_1.8.2-1ubuntu1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32-0.1ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libmpx2_8.2.0-9ubuntu1 libncurses6_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4-1 libnpth0_1.6-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-11 libperl5.26_5.26.2-7 libperl5.28_5.28.0-3 libpipeline1_1.5.0-1 libpng16-16_1.6.34-2 libpopt-dev_1.16-11 libpopt0_1.16-11 libprocps7_2:3.3.15-2ubuntu1 libprotobuf-dev_3.0.0-9.1ubuntu4 libprotobuf-lite10_3.0.0-9.1ubuntu4 libprotobuf10_3.0.0-9.1ubuntu4 libprotoc10_3.0.0-9.1ubuntu4 libpthread-stubs0-dev_0.3-4 libquadmath0_8.2.0-9ubuntu1 libreadline7_7.0-5 libseccomp2_2.3.3-3ubuntu2 libselinux1_2.8-1build2 libsemanage-common_2.8-1build2 libsemanage1_2.8-1build2 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsm-dev_2:1.2.2-1 libsm6_2:1.2.2-1 libsmartcols1_2.32-0.1ubuntu2 libsqlite3-0_3.24.0-1 libss2_1.44.4-2 libssl1.1_1.1.1-1ubuntu2 libstdc++-8-dev_8.2.0-9ubuntu1 libstdc++6_8.2.0-9ubuntu1 libsystemd0_239-7ubuntu10.1 libtasn1-6_4.13-3 libtimedate-perl_2.3000-2 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-4 libtsan0_8.2.0-9ubuntu1 libubsan1_8.2.0-9ubuntu1 libudev1_239-7ubuntu10.1 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.32-0.1ubuntu2 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libx11-dev_2:1.6.7-1 libxau-dev_1:1.0.8-1 libxau6_1:1.0.8-1 libxcb1_1.13.1-1 libxcb1-dev_1.13.1-1 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext-dev_2:1.3.3-1 libxext6_2:1.3.3-1 libxml2_2.9.4+dfsg1-7ubuntu2 libxmu-dev_2:1.1.2-2 libxmu-headers_2:1.1.2-2 libxmu6_2:1.1.2-2 libxt-dev_1:1.1.5-1 libxt6_1:1.1.5-1 libzstd1_1.3.5+dfsg-1ubuntu1 linux-libc-dev_4.18.0-11.12 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1ubuntu1 make_4.2.1-1.2 man-db_2.8.4-2build1 mawk_1.3.3-17ubuntu3 mount_2.32-0.1ubuntu2 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.1-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-3 perl_5.28.0-3 perl-base_5.28.0-3 perl-modules-5.26_5.26.2-7 perl-modules-5.28_5.28.0-3 pinentry-curses_1.1.0-1build2 pkg-config_0.29.1-0ubuntu2 pkgbinarymangler_143 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 protobuf-compiler_3.0.0-9.1ubuntu4 readline-common_7.0-5 sbuild-build-depends-anfo-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 systemd_239-7ubuntu10.1 systemd-sysv_239-7ubuntu10.1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tar_1.30+dfsg-2 tzdata_2018g-1 ubuntu-keyring_2018.09.18.1 util-linux_2.32-0.1ubuntu2 x11-common_1:7.7+19ubuntu8 x11proto-core-dev_2018.4-4 x11proto-dev_2018.4-4 x11proto-xext-dev_2018.4-4 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.3.5-1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Mon Oct 15 14:55:48 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./anfo_0.98-7.dsc dpkg-source: info: extracting anfo in anfo-0.98 dpkg-source: info: unpacking anfo_0.98.orig.tar.gz dpkg-source: info: unpacking anfo_0.98-7.debian.tar.xz dpkg-source: info: applying 01-silence-narrowing-conversion.patch dpkg-source: info: applying 02-correct-minscore-self-initialization.patch dpkg-source: info: applying 03-include-unistd-forF_OK.patch dpkg-source: info: applying 04-reorder-template-for-new-scope-rules.patch dpkg-source: info: applying 05-autoreconf.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-15625131 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15625131 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15625131 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package anfo dpkg-buildpackage: info: source version 0.98-7 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build anfo-0.98 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf configure.ac:77: warning: LT_INIT was called before AM_PROG_AR /usr/share/aclocal-1.16/ar-lib.m4:13: AM_PROG_AR is expanded from... configure.ac:77: the top level configure.ac:77: warning: LT_INIT was called before AM_PROG_AR /usr/share/aclocal-1.16/ar-lib.m4:13: AM_PROG_AR is expanded from... configure.ac:77: the top level aclocal: overwriting 'm4/libtool.m4' with '/usr/share/aclocal/libtool.m4' aclocal: overwriting 'm4/ltoptions.m4' with '/usr/share/aclocal/ltoptions.m4' aclocal: overwriting 'm4/ltversion.m4' with '/usr/share/aclocal/ltversion.m4' aclocal: overwriting 'm4/lt~obsolete.m4' with '/usr/share/aclocal/lt~obsolete.m4' configure.ac:77: warning: LT_INIT was called before AM_PROG_AR /usr/share/aclocal-1.16/ar-lib.m4:13: AM_PROG_AR is expanded from... configure.ac:77: the top level configure.ac:77: warning: LT_INIT was called before AM_PROG_AR aclocal.m4:70: AM_PROG_AR is expanded from... configure.ac:77: the top level libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:77: warning: LT_INIT was called before AM_PROG_AR /usr/share/aclocal-1.16/ar-lib.m4:13: AM_PROG_AR is expanded from... configure.ac:77: the top level configure.ac:77: warning: LT_INIT was called before AM_PROG_AR /usr/share/aclocal-1.16/ar-lib.m4:13: AM_PROG_AR is expanded from... configure.ac:77: the top level configure.ac:77: warning: LT_INIT was called before AM_PROG_AR aclocal.m4:70: AM_PROG_AR is expanded from... configure.ac:77: the top level configure.ac:77: warning: LT_INIT was called before AM_PROG_AR aclocal.m4:70: AM_PROG_AR is expanded from... configure.ac:77: the top level configure.ac:77: warning: LT_INIT was called before AM_PROG_AR aclocal.m4:70: AM_PROG_AR is expanded from... configure.ac:77: the top level configure.ac:77: installing './ar-lib' configure.ac:12: installing './compile' configure.ac:6: installing './missing' src/Makefile.am: installing './depcomp' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for protoc... /usr/bin/protoc checking for library containing exp... none required checking for library containing log1p... none required checking for poptGetContext in -lpopt... yes checking for deflate in -lz... yes checking for BZ2_bzCompress in -lbz2... yes checking for Elk_Init in -lelk... yes checking popt.h usability... yes checking popt.h presence... yes checking for popt.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for protobuf... yes checking google/protobuf/message.h usability... yes checking google/protobuf/message.h presence... yes checking for google/protobuf/message.h... yes checking elk/scheme.h usability... yes checking elk/scheme.h presence... yes checking for elk/scheme.h... yes checking for ANSI C header files... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for working volatile... yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for int32_t... yes checking for int64_t... yes checking for size_t... yes checking for ssize_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for uint8_t... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for strerror... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating man/Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode checking the archiver (ar) interface... ar dh_auto_build make -j4 make[1]: Entering directory '/<>' make all-recursive make[2]: Entering directory '/<>' Making all in src make[3]: Entering directory '/<>/src' protoc -I. -I/usr/include --cpp_out=. config.proto protoc -I. -I/usr/include --cpp_out=. output.proto [libprotobuf WARNING google/protobuf/compiler/parser.cc:547] No syntax specified for the proto file: config.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) [libprotobuf WARNING google/protobuf/compiler/parser.cc:547] No syntax specified for the proto file: output.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) [libprotobuf WARNING google/protobuf/compiler/parser.cc:547] No syntax specified for the proto file: config.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) make all-am make[4]: Entering directory '/<>/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fa2dna.o fa2dna.cc /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o align.lo align.cc /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo_common.lo anfo_common.cc /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o concurrent_stream.lo concurrent_stream.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c align.cc -fPIC -DPIC -o .libs/align.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo_common.cc -fPIC -DPIC -o .libs/anfo_common.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c concurrent_stream.cc -fPIC -DPIC -o .libs/concurrent_stream.o In file included from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: compress_stream.h: In function ‘google::protobuf::io::FileOutputStream* make_output_stream(const char*)’: compress_stream.h:395:7: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::FileOutputStream > fos( ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h: At global scope: stream.h:319:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:323:20: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:345:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:385:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:387:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:414:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:416:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:422:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:747:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:762:21: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:772:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:795:19: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:806:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:821:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:832:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:846:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from concurrent_stream.h:23, from concurrent_stream.cc:1: stream.h:880:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ concurrent_stream.cc: In member function ‘virtual output::Result streams::ConcurrentStream::fetch_result()’: concurrent_stream.cc:178:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr< Result > r( outgoing_[ next_out_++ ] ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ concurrent_stream.cc: In member function ‘void streams::ConcurrentStream::dequeue(streams::Stream*)’: concurrent_stream.cc:212:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr< Result > r( incoming_[ next_in_ ] ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from align.cc:21: compress_stream.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from align.cc:21: compress_stream.h:97:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from align.cc:21: compress_stream.h: In destructor ‘virtual DeflateStream::~DeflateStream()’: compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate] else if( r != Z_OK ) throw zs_.msg ; ^~~ compress_stream.h:198:36: note: in C++11 destructors default to noexcept In file included from stream.h:20, from align.h:22, from align.cc:21: compress_stream.h: At global scope: compress_stream.h:225:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from align.cc:21: compress_stream.h:278:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from align.cc:21: compress_stream.h: In destructor ‘virtual BzipStream::~BzipStream()’: compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate] else if( r < BZ_OK ) throw BzipError( r ) ; ^ compress_stream.h:379:45: note: in C++11 destructors default to noexcept compress_stream.h: In function ‘google::protobuf::io::FileOutputStream* make_output_stream(const char*)’: compress_stream.h:395:7: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::FileOutputStream > fos( ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h: At global scope: stream.h:319:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:323:20: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:345:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:385:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:387:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:414:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:416:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:422:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: compress_stream.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: compress_stream.h:97:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: compress_stream.h: In destructor ‘virtual DeflateStream::~DeflateStream()’: compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate] else if( r != Z_OK ) throw zs_.msg ; ^~~ compress_stream.h:198:36: note: in C++11 destructors default to noexcept In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: compress_stream.h: At global scope: compress_stream.h:225:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: compress_stream.h:278:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:747:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:762:21: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: compress_stream.h: In destructor ‘virtual BzipStream::~BzipStream()’: compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate] else if( r < BZ_OK ) throw BzipError( r ) ; ^ compress_stream.h:379:45: note: in C++11 destructors default to noexcept compress_stream.h: In function ‘google::protobuf::io::FileOutputStream* make_output_stream(const char*)’: compress_stream.h:395:7: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::FileOutputStream > fos( ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:772:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:795:19: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:806:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:821:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:832:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:846:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from align.cc:21: stream.h:880:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h: At global scope: stream.h:319:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:323:20: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:345:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:385:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:387:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:414:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:416:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:422:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:747:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:762:21: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:772:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:795:19: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:806:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:821:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:832:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:846:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: stream.h:880:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo_common.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c align.cc -o align.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c concurrent_stream.cc -o concurrent_stream.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ducttape.lo ducttape.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c ducttape.cc -fPIC -DPIC -o .libs/ducttape.o In file included from stream.h:20, from ducttape.h:21, from ducttape.cc:21: compress_stream.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from ducttape.h:21, from ducttape.cc:21: compress_stream.h:97:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from ducttape.h:21, from ducttape.cc:21: compress_stream.h: In destructor ‘virtual DeflateStream::~DeflateStream()’: compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate] else if( r != Z_OK ) throw zs_.msg ; ^~~ compress_stream.h:198:36: note: in C++11 destructors default to noexcept In file included from stream.h:20, from ducttape.h:21, from ducttape.cc:21: compress_stream.h: At global scope: compress_stream.h:225:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from ducttape.h:21, from ducttape.cc:21: compress_stream.h:278:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from ducttape.h:21, from ducttape.cc:21: compress_stream.h: In destructor ‘virtual BzipStream::~BzipStream()’: compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate] else if( r < BZ_OK ) throw BzipError( r ) ; ^ compress_stream.h:379:45: note: in C++11 destructors default to noexcept compress_stream.h: In function ‘google::protobuf::io::FileOutputStream* make_output_stream(const char*)’: compress_stream.h:395:7: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::FileOutputStream > fos( ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h: At global scope: stream.h:319:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:323:20: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:345:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:385:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:387:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:414:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:416:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:422:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:747:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:762:21: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:772:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:795:19: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:806:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:821:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:832:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:846:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from ducttape.cc:21: stream.h:880:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.cc:21: ducttape.h:139:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from ducttape.h:20, from ducttape.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o index.lo index.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c index.cc -fPIC -DPIC -o .libs/index.o /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o misc_streams.lo misc_streams.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_streams.cc -fPIC -DPIC -o .libs/misc_streams.o In file included from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: compress_stream.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: compress_stream.h:97:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: compress_stream.h: In destructor ‘virtual DeflateStream::~DeflateStream()’: compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate] else if( r != Z_OK ) throw zs_.msg ; ^~~ compress_stream.h:198:36: note: in C++11 destructors default to noexcept In file included from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: compress_stream.h: At global scope: compress_stream.h:225:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: compress_stream.h:278:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: compress_stream.h: In destructor ‘virtual BzipStream::~BzipStream()’: compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate] else if( r < BZ_OK ) throw BzipError( r ) ; ^ compress_stream.h:379:45: note: in C++11 destructors default to noexcept compress_stream.h: In function ‘google::protobuf::io::FileOutputStream* make_output_stream(const char*)’: compress_stream.h:395:7: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::FileOutputStream > fos( ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h: At global scope: stream.h:319:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:323:20: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:345:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:385:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:387:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:414:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:416:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:422:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:747:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:762:21: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:772:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:795:19: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:806:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:821:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:832:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:846:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from misc_streams.cc:5: stream.h:880:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ misc_streams.cc: In constructor ‘streams::RegionFilter::RegionFilter(const std::pair*, std::__cxx11::basic_string >&)’: misc_streams.cc:489:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr< istream > deffile( p.first ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo_common.cc -o anfo_common.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c ducttape.cc -o ducttape.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c index.cc -o index.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_streams.cc -o misc_streams.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o output_streams.lo output_streams.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c output_streams.cc -fPIC -DPIC -o .libs/output_streams.o In file included from stream.h:20, from output_streams.h:21, from output_streams.cc:21: compress_stream.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from output_streams.h:21, from output_streams.cc:21: compress_stream.h:97:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from output_streams.h:21, from output_streams.cc:21: compress_stream.h: In destructor ‘virtual DeflateStream::~DeflateStream()’: compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate] else if( r != Z_OK ) throw zs_.msg ; ^~~ compress_stream.h:198:36: note: in C++11 destructors default to noexcept In file included from stream.h:20, from output_streams.h:21, from output_streams.cc:21: compress_stream.h: At global scope: compress_stream.h:225:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from output_streams.h:21, from output_streams.cc:21: compress_stream.h:278:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from output_streams.h:21, from output_streams.cc:21: compress_stream.h: In destructor ‘virtual BzipStream::~BzipStream()’: compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate] else if( r < BZ_OK ) throw BzipError( r ) ; ^ compress_stream.h:379:45: note: in C++11 destructors default to noexcept compress_stream.h: In function ‘google::protobuf::io::FileOutputStream* make_output_stream(const char*)’: compress_stream.h:395:7: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::FileOutputStream > fos( ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h: At global scope: stream.h:319:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:323:20: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:345:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:385:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:387:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:414:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:416:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:422:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:747:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:762:21: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:772:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:795:19: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:806:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:821:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:832:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:846:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.h:21, from output_streams.cc:21: stream.h:880:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.cc:21: output_streams.h:45:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.cc:21: output_streams.h:72:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.cc:21: output_streams.h:123:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.cc:21: output_streams.h:138:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.cc:21: output_streams.h:149:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from output_streams.cc:21: output_streams.h:176:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from config.pb.h:26, from index.h:20, from output_streams.h:20, from output_streams.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence.lo sequence.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c sequence.cc -fPIC -DPIC -o .libs/sequence.o /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stream.lo stream.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c stream.cc -fPIC -DPIC -o .libs/stream.o In file included from stream.cc:21: compress_stream.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.cc:21: compress_stream.h:97:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.cc:21: compress_stream.h: In destructor ‘virtual DeflateStream::~DeflateStream()’: compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate] else if( r != Z_OK ) throw zs_.msg ; ^~~ compress_stream.h:198:36: note: in C++11 destructors default to noexcept In file included from stream.cc:21: compress_stream.h: At global scope: compress_stream.h:225:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.cc:21: compress_stream.h:278:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.cc:21: compress_stream.h: In destructor ‘virtual BzipStream::~BzipStream()’: compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate] else if( r < BZ_OK ) throw BzipError( r ) ; ^ compress_stream.h:379:45: note: in C++11 destructors default to noexcept compress_stream.h: In function ‘google::protobuf::io::FileOutputStream* make_output_stream(const char*)’: compress_stream.h:395:7: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::FileOutputStream > fos( ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from sequence.cc:23: compress_stream.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from sequence.cc:23: compress_stream.h:97:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from sequence.cc:23: compress_stream.h: In destructor ‘virtual DeflateStream::~DeflateStream()’: compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate] else if( r != Z_OK ) throw zs_.msg ; ^~~ compress_stream.h:198:36: note: in C++11 destructors default to noexcept In file included from stream.h:20, from sequence.cc:23: compress_stream.h: At global scope: compress_stream.h:225:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from sequence.cc:23: compress_stream.h:278:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from sequence.cc:23: compress_stream.h: In destructor ‘virtual BzipStream::~BzipStream()’: compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate] else if( r < BZ_OK ) throw BzipError( r ) ; ^ compress_stream.h:379:45: note: in C++11 destructors default to noexcept compress_stream.h: In function ‘google::protobuf::io::FileOutputStream* make_output_stream(const char*)’: compress_stream.h:395:7: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::FileOutputStream > fos( ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h: At global scope: stream.h:319:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:323:20: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:345:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:385:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:387:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:414:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:416:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:422:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:747:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:762:21: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:772:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:795:19: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:806:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:821:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:832:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:846:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from sequence.cc:23: stream.h:880:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from sequence.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h: At global scope: stream.h:319:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:323:20: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:345:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:385:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:387:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:414:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:416:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:422:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:747:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:762:21: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:772:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:795:19: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:806:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:821:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:832:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:846:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h:880:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ stream.cc:81:30: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] AnfoReader::AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ stream.cc:421:36: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] ChunkedReader::ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ stream.cc:1093:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ stream.cc:1114:29: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] StreamWithProgress( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, int64_t total ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ stream.cc:1149:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] StreamHolder make_input_stream_( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, bool solexa_scores, char origin, const string& genome ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ stream.cc: In function ‘streams::StreamHolder streams::{anonymous}::make_input_stream_(std::auto_ptr, const string&, bool, char, const string&)’: stream.cc:1179:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > bs( new BunzipStream( is ) ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ stream.cc:1189:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > zs( new InflateStream( is ) ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ stream.cc: In member function ‘virtual output::Header streams::UniversalReader::fetch_header()’: stream.cc:1233:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::FileInputStream > s( new google::protobuf::io::FileInputStream( fd ) ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ stream.cc:1238:12: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr(s), name_, st.st_size ) ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ stream.cc: At global scope: stream.cc:1378:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BamReader::BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from stream.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo util.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c util.cc -fPIC -DPIC -o .libs/util.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c output_streams.cc -o output_streams.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c sequence.cc -o sequence.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c util.cc -o util.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo-elk.lo anfo-elk.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo-elk.cc -fPIC -DPIC -o .libs/anfo-elk.o /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fastlz.lo fastlz.c In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: compress_stream.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: compress_stream.h:97:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: compress_stream.h: In destructor ‘virtual DeflateStream::~DeflateStream()’: compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate] else if( r != Z_OK ) throw zs_.msg ; ^~~ compress_stream.h:198:36: note: in C++11 destructors default to noexcept In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: compress_stream.h: At global scope: compress_stream.h:225:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c fastlz.c -fPIC -DPIC -o .libs/fastlz.o In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: compress_stream.h:278:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: compress_stream.h: In destructor ‘virtual BzipStream::~BzipStream()’: compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate] else if( r < BZ_OK ) throw BzipError( r ) ; ^ compress_stream.h:379:45: note: in C++11 destructors default to noexcept compress_stream.h: In function ‘google::protobuf::io::FileOutputStream* make_output_stream(const char*)’: compress_stream.h:395:7: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::FileOutputStream > fos( ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h: At global scope: stream.h:319:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:323:20: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:345:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:385:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:387:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:414:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:416:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:422:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:747:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:762:21: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:772:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:795:19: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:806:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:821:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:832:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:846:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo-elk.cc:27: stream.h:880:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-elk.cc:28: ducttape.h:139:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c fastlz.c -o fastlz.o >/dev/null 2>&1 In file included from anfo-elk.cc:31: output_streams.h:45:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-elk.cc:31: output_streams.h:72:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-elk.cc:31: output_streams.h:123:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-elk.cc:31: output_streams.h:138:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-elk.cc:31: output_streams.h:149:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-elk.cc:31: output_streams.h:176:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o config.pb.lo config.pb.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c config.pb.cc -fPIC -DPIC -o .libs/config.pb.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c stream.cc -o stream.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o output.pb.lo output.pb.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c output.pb.cc -fPIC -DPIC -o .libs/output.pb.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c config.pb.cc -o config.pb.o >/dev/null 2>&1 g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dnaindex.o dnaindex.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c output.pb.cc -o output.pb.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo-elk.cc -o anfo-elk.o >/dev/null 2>&1 g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo-tool.o anfo-tool.cc g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo.o anfo.cc In file included from anfo-tool.cc:21: compress_stream.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-tool.cc:21: compress_stream.h:97:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-tool.cc:21: compress_stream.h: In destructor ‘virtual DeflateStream::~DeflateStream()’: compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate] else if( r != Z_OK ) throw zs_.msg ; ^~~ compress_stream.h:198:36: note: in C++11 destructors default to noexcept In file included from anfo-tool.cc:21: compress_stream.h: At global scope: compress_stream.h:225:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-tool.cc:21: compress_stream.h:278:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-tool.cc:21: compress_stream.h: In destructor ‘virtual BzipStream::~BzipStream()’: compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate] else if( r < BZ_OK ) throw BzipError( r ) ; ^ compress_stream.h:379:45: note: in C++11 destructors default to noexcept compress_stream.h: In function ‘google::protobuf::io::FileOutputStream* make_output_stream(const char*)’: compress_stream.h:395:7: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::FileOutputStream > fos( ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h: At global scope: stream.h:319:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:323:20: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:345:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:385:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:387:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:414:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:416:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:422:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:747:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:762:21: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:772:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:795:19: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:806:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:821:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:832:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:846:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:880:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-tool.cc:22: ducttape.h:139:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-tool.cc:24: output_streams.h:45:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-tool.cc:24: output_streams.h:72:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-tool.cc:24: output_streams.h:123:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-tool.cc:24: output_streams.h:138:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-tool.cc:24: output_streams.h:149:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from anfo-tool.cc:24: output_streams.h:176:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from anfo-tool.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo.cc:21: compress_stream.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo.cc:21: compress_stream.h:97:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo.cc:21: compress_stream.h: In destructor ‘virtual DeflateStream::~DeflateStream()’: compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate] else if( r != Z_OK ) throw zs_.msg ; ^~~ compress_stream.h:198:36: note: in C++11 destructors default to noexcept In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo.cc:21: compress_stream.h: At global scope: compress_stream.h:225:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo.cc:21: compress_stream.h:278:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from align.h:22, from anfo_common.h:22, from anfo.cc:21: compress_stream.h: In destructor ‘virtual BzipStream::~BzipStream()’: compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate] else if( r < BZ_OK ) throw BzipError( r ) ; ^ compress_stream.h:379:45: note: in C++11 destructors default to noexcept compress_stream.h: In function ‘google::protobuf::io::FileOutputStream* make_output_stream(const char*)’: compress_stream.h:395:7: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::FileOutputStream > fos( ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h: At global scope: stream.h:319:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:323:20: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:345:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:385:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:387:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:414:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:416:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:422:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:747:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:762:21: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:772:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:795:19: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:806:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:821:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:832:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:846:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo.cc:21: stream.h:880:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o index-test.o index-test.cc In file included from index-test.cc:27: compress_stream.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:27: compress_stream.h:97:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:27: compress_stream.h: In destructor ‘virtual DeflateStream::~DeflateStream()’: compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate] else if( r != Z_OK ) throw zs_.msg ; ^~~ compress_stream.h:198:36: note: in C++11 destructors default to noexcept In file included from index-test.cc:27: compress_stream.h: At global scope: compress_stream.h:225:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:27: compress_stream.h:278:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:27: compress_stream.h: In destructor ‘virtual BzipStream::~BzipStream()’: compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate] else if( r < BZ_OK ) throw BzipError( r ) ; ^ compress_stream.h:379:45: note: in C++11 destructors default to noexcept compress_stream.h: In function ‘google::protobuf::io::FileOutputStream* make_output_stream(const char*)’: compress_stream.h:395:7: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::FileOutputStream > fos( ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o file-info.o file-info.cc In file included from index-test.cc:30: stream.h: At global scope: stream.h:319:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:323:20: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:345:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:385:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:387:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:414:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:416:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:422:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:747:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:762:21: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:772:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:795:19: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:806:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:821:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:832:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:846:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from index-test.cc:30: stream.h:880:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47, from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46, from compress_stream.h:23, from index-test.cc:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from file-info.cc:25: compress_stream.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from file-info.cc:25: compress_stream.h:97:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from file-info.cc:25: compress_stream.h: In destructor ‘virtual DeflateStream::~DeflateStream()’: compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate] else if( r != Z_OK ) throw zs_.msg ; ^~~ compress_stream.h:198:36: note: in C++11 destructors default to noexcept In file included from stream.h:20, from file-info.cc:25: compress_stream.h: At global scope: compress_stream.h:225:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from file-info.cc:25: compress_stream.h:278:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from stream.h:20, from file-info.cc:25: compress_stream.h: In destructor ‘virtual BzipStream::~BzipStream()’: compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate] else if( r < BZ_OK ) throw BzipError( r ) ; ^ compress_stream.h:379:45: note: in C++11 destructors default to noexcept compress_stream.h: In function ‘google::protobuf::io::FileOutputStream* make_output_stream(const char*)’: compress_stream.h:395:7: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::FileOutputStream > fos( ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h: At global scope: stream.h:319:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:323:20: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:345:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:385:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:387:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:414:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:416:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:422:23: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:747:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:762:21: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:772:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:795:19: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:806:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:821:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:832:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:846:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from file-info.cc:25: stream.h:880:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from /usr/include/google/protobuf/descriptor.h:57, from /usr/include/google/protobuf/message.h:122, from output.pb.h:26, from sequence.h:32, from align_fwd.h:5, from file-info.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ echo "; DO NOT EDIT THIS FILE! EDIT anfo.scm.in AND RUN MAKE INSTEAD!" > anfo.scm sed -e "s#__LIBDIR__#/usr/lib/x86_64-linux-gnu#g" < ./anfo.scm.in >> anfo.scm /bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o libanfo.la -rpath /usr/lib/x86_64-linux-gnu align.lo anfo_common.lo concurrent_stream.lo ducttape.lo index.lo misc_streams.lo output_streams.lo sequence.lo stream.lo util.lo anfo-elk.lo fastlz.lo config.pb.lo output.pb.lo -lprotobuf -pthread -lpthread -lpthread -lelk -lbz2 -lz -lpopt libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/8/crtbeginS.o .libs/align.o .libs/anfo_common.o .libs/concurrent_stream.o .libs/ducttape.o .libs/index.o .libs/misc_streams.o .libs/output_streams.o .libs/sequence.o .libs/stream.o .libs/util.o .libs/anfo-elk.o .libs/fastlz.o .libs/config.pb.o .libs/output.pb.o -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt -L/usr/lib/gcc/x86_64-linux-gnu/8 -L/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/8/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/8/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/crtn.o -pthread -g -O2 -fstack-protector-strong -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -pthread -Wl,-soname -Wl,libanfo.so.0 -o .libs/libanfo.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libanfo.so.0" && ln -s "libanfo.so.0.0.0" "libanfo.so.0") libtool: link: (cd ".libs" && rm -f "libanfo.so" && ln -s "libanfo.so.0.0.0" "libanfo.so") libtool: link: ar cru .libs/libanfo.a align.o anfo_common.o concurrent_stream.o ducttape.o index.o misc_streams.o output_streams.o sequence.o stream.o util.o anfo-elk.o fastlz.o config.pb.o output.pb.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libanfo.a libtool: link: ( cd ".libs" && rm -f "libanfo.la" && ln -s "../libanfo.la" "libanfo.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o dnaindex dnaindex.o libanfo.la -lprotobuf -pthread -lpthread -lelk -lbz2 -lz -lpopt /bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o fa2dna fa2dna.o libanfo.la -lprotobuf -pthread -lpthread -lelk -lbz2 -lz -lpopt /bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o anfo-tool anfo-tool.o libanfo.la -lprotobuf -pthread -lpthread -lelk -lbz2 -lz -lpopt /bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o anfo anfo.o libanfo.la -lprotobuf -pthread -lpthread -lelk -lbz2 -lz -lpopt libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/anfo-tool anfo-tool.o -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt -pthread libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/dnaindex dnaindex.o -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt -pthread libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/fa2dna fa2dna.o -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt -pthread libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/anfo anfo.o -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt -pthread /bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o index-test index-test.o libanfo.la -lprotobuf -pthread -lpthread -lelk -lbz2 -lz -lpopt /bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o file-info file-info.o libanfo.la -lprotobuf -pthread -lpthread -lelk -lbz2 -lz -lpopt libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/index-test index-test.o -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt -pthread libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/file-info file-info.o -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt -pthread make[4]: Leaving directory '/<>/src' make[3]: Leaving directory '/<>/src' Making all in man make[3]: Entering directory '/<>/man' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/man' make[3]: Entering directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test make -j4 check VERBOSE=1 make[1]: Entering directory '/<>' Making check in src make[2]: Entering directory '/<>/src' make check-am make[3]: Entering directory '/<>/src' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>/src' Making check in man make[2]: Entering directory '/<>/man' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/man' make[2]: Entering directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j1 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' Making install in src make[2]: Entering directory '/<>/src' make install-am make[3]: Entering directory '/<>/src' make[4]: Entering directory '/<>/src' /bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libanfo.la '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libanfo.so.0.0.0 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.so.0.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libanfo.so.0.0.0 libanfo.so.0 || { rm -f libanfo.so.0 && ln -s libanfo.so.0.0.0 libanfo.so.0; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libanfo.so.0.0.0 libanfo.so || { rm -f libanfo.so && ln -s libanfo.so.0.0.0 libanfo.so; }; }) libtool: install: /usr/bin/install -c .libs/libanfo.lai /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.la libtool: install: /usr/bin/install -c .libs/libanfo.a /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.a libtool: install: ranlib /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /bin/mkdir -p '/<>/debian/tmp/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c fa2dna dnaindex anfo-tool anfo '/<>/debian/tmp/usr/bin' libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/fa2dna /<>/debian/tmp/usr/bin/fa2dna libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/dnaindex /<>/debian/tmp/usr/bin/dnaindex libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/anfo-tool /<>/debian/tmp/usr/bin/anfo-tool libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/anfo /<>/debian/tmp/usr/bin/anfo /bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c index-test file-info '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/index-test /<>/debian/tmp/usr/lib/x86_64-linux-gnu/index-test libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/file-info /<>/debian/tmp/usr/lib/x86_64-linux-gnu/file-info /bin/mkdir -p '/<>/debian/tmp/usr/share/anfo' /usr/bin/install -c -m 644 config.proto output.proto '/<>/debian/tmp/usr/share/anfo' /bin/mkdir -p '/<>/debian/tmp/usr/share/elk' /usr/bin/install -c srfi-88.scm srfi-89.scm '/<>/debian/tmp/usr/share/elk' /bin/mkdir -p '/<>/debian/tmp/usr/include/anfo' /usr/bin/install -c -m 644 align.h align_fwd.h anfo_common.h compress_stream.h concurrent_stream.h conffile.h ducttape.h index.h logdom.h misc_streams.h output_streams.h sequence.h stream.h trim.h util.h '/<>/debian/tmp/usr/include/anfo' /bin/mkdir -p '/<>/debian/tmp/usr/share/elk' /usr/bin/install -c anfo.scm '/<>/debian/tmp/usr/share/elk' make[4]: Leaving directory '/<>/src' make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>/src' Making install in man make[2]: Entering directory '/<>/man' make[3]: Entering directory '/<>/man' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 fa2dna.1 dnaindex.1 anfo-sge.1 anfo-tool.1 file-info.1 '/<>/debian/tmp/usr/share/man/man1' make[3]: Leaving directory '/<>/man' make[2]: Leaving directory '/<>/man' make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/<>/debian/tmp/usr/share/doc/anfo' /usr/bin/install -c -m 644 README '/<>/debian/tmp/usr/share/doc/anfo/.' /bin/mkdir -p '/<>/debian/tmp/usr/share/doc/anfo/example' /usr/bin/install -c -m 644 example/ancient.cfg example/default.cfg example/split-anfo.scm example/threebam.scm '/<>/debian/tmp/usr/share/doc/anfo/example' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' rm `find debian/tmp -name '*.la'` d-shlibmove --commit \ --multiarch \ --movedev debian/tmp/usr/include/* usr/include \ debian/tmp/usr/lib/*/libanfo.so Library package automatic movement utility --> libbz2-dev package exists. --> libelk0-dev package exists. --> libprotobuf-dev package exists. --> zlib1g-dev package exists. set -e install -d -m 755 debian/libanfo0-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libanfo0/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.a debian/libanfo0-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.la debian/libanfo0-dev/usr/lib/x86_64-linux-gnu || true mv debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.so debian/libanfo0-dev/usr/lib/x86_64-linux-gnu mv /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.so.0 debian/libanfo0/usr/lib/x86_64-linux-gnu mv /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.so.0.0.0 debian/libanfo0/usr/lib/x86_64-linux-gnu PKGDEV=libanfo0-dev PKGSHL=libanfo0 install -d -m 755 debian/libanfo0-dev/usr/include mv debian/tmp/usr/include/anfo debian/libanfo0-dev/usr/include mv: cannot stat 'debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.la': No such file or directory dh_install mv debian/anfo/usr/lib/* debian/anfo/usr/lib/anfo make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/<>' dh_installman # delete unused manpage find debian/anfo -name anfo-sge.1 -delete make[1]: Leaving directory '/<>' dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian/anfo -perm -5 -type f \( -name '*.scm' \) -print0 2>/dev/null | xargs -0r chmod 644 make[1]: Leaving directory '/<>' dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 pkgstriptranslations: processing libanfo0-dev (in debian/libanfo0-dev); do_strip: , oemstrip: pkgstriptranslations: processing anfo (in debian/anfo); do_strip: , oemstrip: pkgstriptranslations: processing libanfo0 (in debian/libanfo0); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/anfo/DEBIAN/control, package anfo, directory debian/anfo Searching for duplicated docs in dependency libanfo0... pkgstripfiles: processing control file: debian/libanfo0/DEBIAN/control, package libanfo0, directory debian/libanfo0 INFO: pkgstripfiles: waiting for lock (libanfo0) ... symlinking changelog.Debian.gz in anfo to file in libanfo0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package anfo ... pkgstripfiles: No PNG files. dpkg-deb: building package 'anfo' in '../anfo_0.98-7_amd64.deb'. INFO: pkgstriptranslations version 143 pkgstriptranslations: processing anfo-dbgsym (in debian/.debhelper/anfo/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: Running PNG optimization (using 4 cpus) for package libanfo0 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libanfo0' in '../libanfo0_0.98-7_amd64.deb'. pkgstripfiles: processing control file: debian/.debhelper/anfo/dbgsym-root/DEBIAN/control, package anfo-dbgsym, directory debian/.debhelper/anfo/dbgsym-root dpkg-deb: building package 'anfo-dbgsym' in 'debian/.debhelper/scratch-space/build-anfo/anfo-dbgsym_0.98-7_amd64.deb'. Renaming anfo-dbgsym_0.98-7_amd64.deb to anfo-dbgsym_0.98-7_amd64.ddeb INFO: pkgstriptranslations version 143 pkgstriptranslations: processing libanfo0-dbgsym (in debian/.debhelper/libanfo0/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/libanfo0/dbgsym-root/DEBIAN/control, package libanfo0-dbgsym, directory debian/.debhelper/libanfo0/dbgsym-root dpkg-deb: building package 'libanfo0-dbgsym' in 'debian/.debhelper/scratch-space/build-libanfo0/libanfo0-dbgsym_0.98-7_amd64.deb'. Renaming libanfo0-dbgsym_0.98-7_amd64.deb to libanfo0-dbgsym_0.98-7_amd64.ddeb pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libanfo0-dev/DEBIAN/control, package libanfo0-dev, directory debian/libanfo0-dev Searching for duplicated docs in dependency libanfo0... symlinking changelog.Debian.gz in libanfo0-dev to file in libanfo0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libanfo0-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libanfo0-dev' in '../libanfo0-dev_0.98-7_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../anfo_0.98-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build anfo-0.98 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20181109-0722 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ anfo_0.98-7_amd64.changes: -------------------------- Format: 1.8 Date: Mon, 15 Oct 2018 15:41:57 +0200 Source: anfo Binary: anfo libanfo0 libanfo0-dev Architecture: amd64 Version: 0.98-7 Distribution: disco-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: anfo - Short Read Aligner/Mapper from MPG libanfo0 - Library for Short Read Aligner/Mapper from MPG libanfo0-dev - Development files for Short Read Aligner/Mapper from MPG Changes: anfo (0.98-7) unstable; urgency=medium . * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 Checksums-Sha1: d061db0749b3626f32a8edbdedf9c280817b51f6 1323620 anfo-dbgsym_0.98-7_amd64.ddeb 05122b0aea01d52294432723dce54e85b3216918 7306 anfo_0.98-7_amd64.buildinfo fe03f01c85b5d7c306f82a3285bc6a01ed91cd8c 117068 anfo_0.98-7_amd64.deb 6c0f491657b9be23041c6bc0fb60ad76f8c373f1 3426000 libanfo0-dbgsym_0.98-7_amd64.ddeb 2c19ebf0218263c21d187a44436a8067fe4966df 347688 libanfo0-dev_0.98-7_amd64.deb 1f81a8c9acf0e316b7570e9bf71e2da6a1589284 280652 libanfo0_0.98-7_amd64.deb Checksums-Sha256: 9f66aa5892e8ef0c03a268dc3469ef5720cb62334acbb310a95ccf2ed37bfb9c 1323620 anfo-dbgsym_0.98-7_amd64.ddeb 0f16fb85ffbb589be4ef79b9a1c3aaa45c13b681dd6f8dd4ebd386f8e84aacc9 7306 anfo_0.98-7_amd64.buildinfo 86a969f6b5119e7c3fc3e4b081ca868f0b8cf7282685a00ad384c4a1663b3ae5 117068 anfo_0.98-7_amd64.deb 11fe2deb2ce98678c4c76db31a7619b6970d92cc55cafe5e849858437d43ec26 3426000 libanfo0-dbgsym_0.98-7_amd64.ddeb 908635888dc665da42943a24d5d0ed8e0872160d53cb0c090e38f4c769662705 347688 libanfo0-dev_0.98-7_amd64.deb 6fe4b9e16b102636fc29efcbbfff8e786007801ac29236222aed132ff79337f2 280652 libanfo0_0.98-7_amd64.deb Files: d4ba8c77de810e0a82a82be00cde74dd 1323620 debug optional anfo-dbgsym_0.98-7_amd64.ddeb 5b0636f82daf704c6cd9eed68bfbd6c7 7306 science optional anfo_0.98-7_amd64.buildinfo 21ce1d69fe3d3c613628ba0e3bb1fb11 117068 science optional anfo_0.98-7_amd64.deb 961b472bf168383a51c2024a395f6e79 3426000 debug optional libanfo0-dbgsym_0.98-7_amd64.ddeb 6938cd821927e61edfa250e985b9e5aa 347688 libdevel optional libanfo0-dev_0.98-7_amd64.deb 5a9819ff24c74cb3b61a4f2f006571e4 280652 libs optional libanfo0_0.98-7_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ anfo_0.98-7_amd64.deb --------------------- new debian package, version 2.0. size 117068 bytes: control archive=1512 bytes. 935 bytes, 17 lines control 1435 bytes, 23 lines md5sums Package: anfo Version: 0.98-7 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 446 Depends: libanfo0, libc6 (>= 2.27), libelk0, libgcc1 (>= 1:3.0), libpopt0 (>= 1.14), libprotobuf10, libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: http://bioinf.eva.mpg.de/anfo/ Description: Short Read Aligner/Mapper from MPG Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes more after BLAST/BLAT. It's most useful for the alignment of sequencing reads where the DNA sequence is somehow modified (think ancient DNA or bisulphite treatment) and/or there is more divergence between sample and reference than what fast mappers will handle gracefully (say the reference genome is missing and a related species is used instead). drwxr-xr-x root/root 0 2018-10-15 13:41 ./ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/bin/ -rwxr-xr-x root/root 47264 2018-10-15 13:41 ./usr/bin/anfo -rwxr-xr-x root/root 158928 2018-10-15 13:41 ./usr/bin/anfo-tool -rwxr-xr-x root/root 51360 2018-10-15 13:41 ./usr/bin/dnaindex -rwxr-xr-x root/root 43168 2018-10-15 13:41 ./usr/bin/fa2dna drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/anfo/ -rwxr-xr-x root/root 22688 2018-10-15 13:41 ./usr/lib/anfo/file-info -rwxr-xr-x root/root 39072 2018-10-15 13:41 ./usr/lib/anfo/index-test drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/anfo/ -rw-r--r-- root/root 6784 2018-10-15 13:41 ./usr/share/anfo/config.proto -rw-r--r-- root/root 14546 2018-10-15 13:41 ./usr/share/anfo/output.proto drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/anfo/ -rw-r--r-- root/root 909 2018-10-15 13:41 ./usr/share/doc/anfo/README.Debian -rw-r--r-- root/root 2441 2018-10-15 13:41 ./usr/share/doc/anfo/README.gz lrwxrwxrwx root/root 0 2018-10-15 13:41 ./usr/share/doc/anfo/changelog.Debian.gz -> ../libanfo0/changelog.Debian.gz -rw-r--r-- root/root 2550 2018-10-15 13:41 ./usr/share/doc/anfo/copyright drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/anfo/example/ -rw-r--r-- root/root 1807 2018-10-15 13:41 ./usr/share/doc/anfo/example/ancient.cfg -rw-r--r-- root/root 2056 2018-10-15 13:41 ./usr/share/doc/anfo/example/default.cfg -rw-r--r-- root/root 521 2018-10-15 13:41 ./usr/share/doc/anfo/example/split-anfo.scm -rw-r--r-- root/root 567 2018-10-15 13:41 ./usr/share/doc/anfo/example/threebam.scm drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/elk/ -rw-r--r-- root/root 9714 2018-10-15 13:41 ./usr/share/elk/anfo.scm -rw-r--r-- root/root 2593 2018-10-15 13:41 ./usr/share/elk/srfi-88.scm -rw-r--r-- root/root 12138 2018-10-15 13:41 ./usr/share/elk/srfi-89.scm drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/man/ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/man/man1/ -rw-r--r-- root/root 4029 2018-10-15 13:41 ./usr/share/man/man1/anfo-tool.1.gz -rw-r--r-- root/root 1616 2018-10-15 13:41 ./usr/share/man/man1/anfo.1.gz -rw-r--r-- root/root 1684 2018-10-15 13:41 ./usr/share/man/man1/dnaindex.1.gz -rw-r--r-- root/root 1202 2018-10-15 13:41 ./usr/share/man/man1/fa2dna.1.gz -rw-r--r-- root/root 634 2018-10-15 13:41 ./usr/share/man/man1/file-info.1.gz libanfo0-dev_0.98-7_amd64.deb ----------------------------- new debian package, version 2.0. size 347688 bytes: control archive=1412 bytes. 1073 bytes, 23 lines control 1082 bytes, 17 lines md5sums Package: libanfo0-dev Source: anfo Version: 0.98-7 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2275 Depends: libanfo0 (= 0.98-7), libbz2-dev, libelk0-dev, libprotobuf-dev, zlib1g-dev Conflicts: libanfo-dev Provides: libanfo-dev Section: libdevel Priority: optional Homepage: http://bioinf.eva.mpg.de/anfo/ Description: Development files for Short Read Aligner/Mapper from MPG Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes more after BLAST/BLAT. It's most useful for the alignment of sequencing reads where the DNA sequence is somehow modified (think ancient DNA or bisulphite treatment) and/or there is more divergence between sample and reference than what fast mappers will handle gracefully (say the reference genome is missing and a related species is used instead). . This package contains the development files that might be used in connection with the anfo binaries. drwxr-xr-x root/root 0 2018-10-15 13:41 ./ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/include/ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/include/anfo/ -rw-r--r-- root/root 14361 2018-10-15 13:41 ./usr/include/anfo/align.h -rw-r--r-- root/root 2595 2018-10-15 13:41 ./usr/include/anfo/align_fwd.h -rw-r--r-- root/root 3399 2018-10-15 13:41 ./usr/include/anfo/anfo_common.h -rw-r--r-- root/root 11973 2018-10-15 13:41 ./usr/include/anfo/compress_stream.h -rw-r--r-- root/root 4906 2018-10-15 13:41 ./usr/include/anfo/concurrent_stream.h -rw-r--r-- root/root 2979 2018-10-15 13:41 ./usr/include/anfo/conffile.h -rw-r--r-- root/root 5051 2018-10-15 13:41 ./usr/include/anfo/ducttape.h -rw-r--r-- root/root 17630 2018-10-15 13:41 ./usr/include/anfo/index.h -rw-r--r-- root/root 5881 2018-10-15 13:41 ./usr/include/anfo/logdom.h -rw-r--r-- root/root 22028 2018-10-15 13:41 ./usr/include/anfo/misc_streams.h -rw-r--r-- root/root 5942 2018-10-15 13:41 ./usr/include/anfo/output_streams.h -rw-r--r-- root/root 14774 2018-10-15 13:41 ./usr/include/anfo/sequence.h -rw-r--r-- root/root 30889 2018-10-15 13:41 ./usr/include/anfo/stream.h -rw-r--r-- root/root 5292 2018-10-15 13:41 ./usr/include/anfo/trim.h -rw-r--r-- root/root 9473 2018-10-15 13:41 ./usr/include/anfo/util.h drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 2149334 2018-10-15 13:41 ./usr/lib/x86_64-linux-gnu/libanfo.a lrwxrwxrwx root/root 0 2018-10-15 13:41 ./usr/lib/x86_64-linux-gnu/libanfo.so -> libanfo.so.0.0.0 drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/libanfo0-dev/ lrwxrwxrwx root/root 0 2018-10-15 13:41 ./usr/share/doc/libanfo0-dev/changelog.Debian.gz -> ../libanfo0/changelog.Debian.gz -rw-r--r-- root/root 2550 2018-10-15 13:41 ./usr/share/doc/libanfo0-dev/copyright libanfo0_0.98-7_amd64.deb ------------------------- new debian package, version 2.0. size 280652 bytes: control archive=1112 bytes. 1012 bytes, 20 lines control 220 bytes, 3 lines md5sums 19 bytes, 1 lines shlibs 74 bytes, 2 lines triggers Package: libanfo0 Source: anfo Version: 0.98-7 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 938 Depends: libbz2-1.0, libc6 (>= 2.27), libelk0, libgcc1 (>= 1:3.0), libprotobuf10, libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.0) Section: libs Priority: optional Homepage: http://bioinf.eva.mpg.de/anfo/ Description: Library for Short Read Aligner/Mapper from MPG Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes more after BLAST/BLAT. It's most useful for the alignment of sequencing reads where the DNA sequence is somehow modified (think ancient DNA or bisulphite treatment) and/or there is more divergence between sample and reference than what fast mappers will handle gracefully (say the reference genome is missing and a related species is used instead). . This package contains the dynamic library for the anfo binaries. drwxr-xr-x root/root 0 2018-10-15 13:41 ./ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2018-10-15 13:41 ./usr/lib/x86_64-linux-gnu/libanfo.so.0 -> libanfo.so.0.0.0 -rw-r--r-- root/root 944360 2018-10-15 13:41 ./usr/lib/x86_64-linux-gnu/libanfo.so.0.0.0 drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/libanfo0/ -rw-r--r-- root/root 1006 2018-10-15 13:41 ./usr/share/doc/libanfo0/changelog.Debian.gz -rw-r--r-- root/root 2550 2018-10-15 13:41 ./usr/share/doc/libanfo0/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 154356 Build-Time: 84 Distribution: disco-proposed Host Architecture: amd64 Install-Time: 12 Job: anfo_0.98-7.dsc Machine Architecture: amd64 Package: anfo Package-Time: 97 Source-Version: 0.98-7 Space: 154356 Status: successful Version: 0.98-7 -------------------------------------------------------------------------------- Finished at 20181109-0722 Build needed 00:01:37, 154356k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15625131 Scanning for processes to kill in build PACKAGEBUILD-15625131