I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 7 00:01:01 -12 2021 I: pbuilder-time-stamp: 1625659261 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [anfo_0.98-7.dsc] I: copying [./anfo_0.98.orig.tar.gz] I: copying [./anfo_0.98-7.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Oct 15 02:55:48 2018 -12 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: using patch list from debian/patches/series 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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/54581/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='4f0375ef3a384aec824ce5181d6b14a9' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='54581' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.JJXvOLF4it/pbuilderrc_hoKy --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.JJXvOLF4it/b1 --logfile b1/build.log anfo_0.98-7.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 6 20:24 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/54581/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. 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 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libpopt-dev; however: Package libpopt-dev is not installed. pbuilder-satisfydepends-dummy depends on libprotobuf-dev; however: Package libprotobuf-dev is not installed. pbuilder-satisfydepends-dummy depends on libelk0-dev; however: Package libelk0-dev is not installed. pbuilder-satisfydepends-dummy depends on libelk0; however: Package libelk0 is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on protobuf-compiler; however: Package protobuf-compiler is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs (>= 0.77); however: Package d-shlibs is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libbz2-dev{a} libcroco3{a} libelf-dev{a} libelf1{a} libelk0{a} libelk0-dev{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libice-dev{a} libice6{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libpopt-dev{a} libpopt0{a} libprotobuf-dev{a} libprotobuf-lite17{a} libprotobuf17{a} libprotoc17{a} libpthread-stubs0-dev{a} libsigsegv2{a} libsm-dev{a} libsm6{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libx11-dev{a} libxau-dev{a} libxau6{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxml2{a} libxmu-dev{a} libxmu-headers{a} libxmu6{a} libxt-dev{a} libxt6{a} lsb-base{a} m4{a} man-db{a} pkg-config{a} po-debconf{a} protobuf-compiler{a} sensible-utils{a} x11-common{a} x11proto-core-dev{a} x11proto-dev{a} x11proto-xext-dev{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 75 newly installed, 0 to remove and 0 not upgraded. Need to get 26.8 MB of archives. After unpacking 102 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 d-shlibs all 0.84 [17.2 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libbz2-dev amd64 1.0.6-9.2~deb10u1 [30.2 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libelf-dev amd64 0.176-1.1 [72.1 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u2 [299 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u2 [757 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libxt6 amd64 1:1.1.5-1+b3 [190 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libxmu6 amd64 2:1.1.2-2+b3 [60.8 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libelk0 amd64 3.99.8-4.2+b1 [166 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 xorg-sgml-doctools all 1:1.11-1 [21.9 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 x11proto-dev all 2018.4-4 [251 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 x11proto-core-dev all 2018.4-4 [3128 B] Get: 54 http://deb.debian.org/debian buster/main amd64 libxau-dev amd64 1:1.0.8-1+b2 [23.1 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 xtrans-dev all 1.3.5-1 [100 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get: 58 http://deb.debian.org/debian buster/main amd64 libxcb1-dev amd64 1.13.1-2 [174 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libx11-dev amd64 2:1.6.7-1+deb10u2 [825 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 x11proto-xext-dev all 2018.4-4 [3128 B] Get: 61 http://deb.debian.org/debian buster/main amd64 libxext-dev amd64 2:1.3.3-1+b2 [107 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libice-dev amd64 2:1.0.9-2 [66.8 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libsm-dev amd64 2:1.2.3-1 [38.0 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libxt-dev amd64 1:1.1.5-1+b3 [426 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libxmu-headers all 2:1.1.2-2 [51.9 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libxmu-dev amd64 2:1.1.2-2+b3 [66.3 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libelk0-dev amd64 3.99.8-4.2+b1 [193 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libpopt0 amd64 1.16-12 [49.4 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libpopt-dev amd64 1.16-12 [51.0 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libprotobuf17 amd64 3.6.1.3-2 [814 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libprotobuf-lite17 amd64 3.6.1.3-2 [167 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libprotobuf-dev amd64 3.6.1.3-2 [1130 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libprotoc17 amd64 3.6.1.3-2 [665 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 pkg-config amd64 0.29-6 [63.5 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 protobuf-compiler amd64 3.6.1.3-2 [64.9 kB] Fetched 26.8 MB in 1s (51.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. 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Setting up autotools-dev (20180224.1) ... Setting up libx11-data (2:1.6.7-1+deb10u2) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up pkg-config (0.29-6) ... Setting up d-shlibs (0.84) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up xorg-sgml-doctools (1:1.11-1) ... Setting up libprotobuf17:amd64 (3.6.1.3-2) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up libpopt0:amd64 (1.16-12) ... Setting up libbz2-dev:amd64 (1.0.6-9.2~deb10u1) ... Setting up x11proto-dev (2018.4-4) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libice6:amd64 (2:1.0.9-2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up libprotoc17:amd64 (3.6.1.3-2) ... Setting up libxau-dev:amd64 (1:1.0.8-1+b2) ... Setting up protobuf-compiler (3.6.1.3-2) ... Setting up libice-dev:amd64 (2:1.0.9-2) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up libpopt-dev:amd64 (1.16-12) ... Setting up libprotobuf-dev:amd64 (3.6.1.3-2) ... Setting up libxdmcp-dev:amd64 (1:1.1.2-3) ... Setting up x11proto-core-dev (2018.4-4) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libelf-dev:amd64 (0.176-1.1) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up x11proto-xext-dev (2018.4-4) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libx11-6:amd64 (2:1.6.7-1+deb10u2) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libxcb1-dev:amd64 (1.13.1-2) ... Setting up libsm-dev:amd64 (2:1.2.3-1) ... Setting up libx11-dev:amd64 (2:1.6.7-1+deb10u2) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxt6:amd64 (1:1.1.5-1+b3) ... Setting up libxext-dev:amd64 (2:1.3.3-1+b2) ... Setting up libxmu-headers (2:1.1.2-2) ... Setting up libxmu6:amd64 (2:1.1.2-2+b3) ... Setting up po-debconf (1.0.21) ... Setting up libxt-dev:amd64 (1:1.1.5-1+b3) ... Setting up libelk0 (3.99.8-4.2+b1) ... Setting up libxmu-dev:amd64 (2:1.1.2-2+b3) ... Setting up libelk0-dev (3.99.8-4.2+b1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/anfo-0.98/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package anfo dpkg-buildpackage: info: source version 0.98-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . 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 -j15 make[1]: Entering directory '/build/anfo-0.98' make all-recursive make[2]: Entering directory '/build/anfo-0.98' Making all in src make[3]: Entering directory '/build/anfo-0.98/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:562] 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:562] 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:562] 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 '/build/anfo-0.98/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -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 -ffile-prefix-map=/build/anfo-0.98=. -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 -ffile-prefix-map=/build/anfo-0.98=. -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 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat 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-fstack-protector-strong -Wformat -Werror=format-security -c -o output_streams.lo output_streams.cc /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence.lo sequence.cc /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stream.lo stream.cc /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo util.cc /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo-elk.lo anfo-elk.cc /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fastlz.lo fastlz.c /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o config.pb.lo config.pb.cc /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -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 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_streams.cc -fPIC -DPIC -o .libs/misc_streams.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -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 -ffile-prefix-map=/build/anfo-0.98=. -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 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c output_streams.cc -fPIC -DPIC -o .libs/output_streams.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c ducttape.cc -fPIC -DPIC -o .libs/ducttape.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c index.cc -fPIC -DPIC -o .libs/index.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c concurrent_stream.cc -fPIC -DPIC -o .libs/concurrent_stream.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c sequence.cc -fPIC -DPIC -o .libs/sequence.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c util.cc -fPIC -DPIC -o .libs/util.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c fastlz.c -fPIC -DPIC -o .libs/fastlz.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c stream.cc -fPIC -DPIC -o .libs/stream.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo-elk.cc -fPIC -DPIC -o .libs/anfo-elk.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -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 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c output.pb.cc -fPIC -DPIC -o .libs/output.pb.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c fastlz.c -o fastlz.o >/dev/null 2>&1 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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; ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dnaindex.o dnaindex.cc 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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.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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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: 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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: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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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; ^~~~~~~~ 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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: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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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: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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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 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/stubs/common.h:41, from config.pb.h:9, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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/stubs/common.h:41, from config.pb.h:9, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c util.cc -o util.o >/dev/null 2>&1 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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; ^~~~~~~~ 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, from sequence.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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, from sequence.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 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c align.cc -o align.o >/dev/null 2>&1 g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo-tool.o anfo-tool.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c concurrent_stream.cc -o concurrent_stream.o >/dev/null 2>&1 g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, from anfo-tool.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 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o index-test.o index-test.cc 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, from anfo-tool.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 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c output_streams.cc -o output_streams.o >/dev/null 2>&1 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, from anfo-tool.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 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c ducttape.cc -o ducttape.o >/dev/null 2>&1 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, from index-test.cc:27: /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 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_streams.cc -o misc_streams.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c sequence.cc -o sequence.o >/dev/null 2>&1 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o file-info.o file-info.cc 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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; ^~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c index.cc -o index.o >/dev/null 2>&1 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from compress_stream.h:22, from index-test.cc:27: /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 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo_common.cc -o anfo_common.o >/dev/null 2>&1 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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c config.pb.cc -o config.pb.o >/dev/null 2>&1 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:111, from sequence.h:30, 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; ^~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c stream.cc -o stream.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo-elk.cc -o anfo-elk.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c output.pb.cc -o output.pb.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -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 -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,-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 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fa2dna fa2dna.o libanfo.la -lprotobuf -pthread -lelk -lbz2 -lz -lpopt /bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o dnaindex dnaindex.o libanfo.la -lprotobuf -pthread -lelk -lbz2 -lz -lpopt /bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o anfo-tool anfo-tool.o libanfo.la -lprotobuf -pthread -lelk -lbz2 -lz -lpopt /bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o anfo anfo.o libanfo.la -lprotobuf -pthread -lelk -lbz2 -lz -lpopt /bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o index-test index-test.o libanfo.la -lprotobuf -pthread -lelk -lbz2 -lz -lpopt /bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o file-info file-info.o libanfo.la -lprotobuf -pthread -lelk -lbz2 -lz -lpopt libtool: link: g++ -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/fa2dna fa2dna.o -pthread ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread libtool: link: g++ -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/dnaindex dnaindex.o -pthread ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread libtool: link: g++ -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/anfo anfo.o -pthread ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread libtool: link: g++ -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/anfo-tool anfo-tool.o -pthread ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread libtool: link: g++ -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/index-test index-test.o -pthread ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread libtool: link: g++ -pthread -g -O2 -ffile-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/file-info file-info.o -pthread ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread make[4]: Leaving directory '/build/anfo-0.98/src' make[3]: Leaving directory '/build/anfo-0.98/src' Making all in man make[3]: Entering directory '/build/anfo-0.98/man' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/anfo-0.98/man' make[3]: Entering directory '/build/anfo-0.98' make[3]: Leaving directory '/build/anfo-0.98' make[2]: Leaving directory '/build/anfo-0.98' make[1]: Leaving directory '/build/anfo-0.98' dh_auto_test make -j15 check VERBOSE=1 make[1]: Entering directory '/build/anfo-0.98' Making check in src make[2]: Entering directory '/build/anfo-0.98/src' make check-am make[3]: Entering directory '/build/anfo-0.98/src' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/anfo-0.98/src' make[2]: Leaving directory '/build/anfo-0.98/src' Making check in man make[2]: Entering directory '/build/anfo-0.98/man' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/anfo-0.98/man' make[2]: Entering directory '/build/anfo-0.98' make[2]: Leaving directory '/build/anfo-0.98' make[1]: Leaving directory '/build/anfo-0.98' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j1 install DESTDIR=/build/anfo-0.98/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/anfo-0.98' Making install in src make[2]: Entering directory '/build/anfo-0.98/src' make install-am make[3]: Entering directory '/build/anfo-0.98/src' make[4]: Entering directory '/build/anfo-0.98/src' /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libanfo.la '/build/anfo-0.98/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libanfo.so.0.0.0 /build/anfo-0.98/debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.so.0.0.0 libtool: install: (cd /build/anfo-0.98/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 /build/anfo-0.98/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 /build/anfo-0.98/debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.la libtool: install: /usr/bin/install -c .libs/libanfo.a /build/anfo-0.98/debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.a libtool: install: chmod 644 /build/anfo-0.98/debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.a libtool: install: ranlib /build/anfo-0.98/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 '/build/anfo-0.98/debian/tmp/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c fa2dna dnaindex anfo-tool anfo '/build/anfo-0.98/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 /build/anfo-0.98/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 /build/anfo-0.98/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 /build/anfo-0.98/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 /build/anfo-0.98/debian/tmp/usr/bin/anfo /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c index-test file-info '/build/anfo-0.98/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 /build/anfo-0.98/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 /build/anfo-0.98/debian/tmp/usr/lib/x86_64-linux-gnu/file-info /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/anfo' /usr/bin/install -c -m 644 config.proto output.proto '/build/anfo-0.98/debian/tmp/usr/share/anfo' /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/elk' /usr/bin/install -c srfi-88.scm srfi-89.scm '/build/anfo-0.98/debian/tmp/usr/share/elk' /bin/mkdir -p '/build/anfo-0.98/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 '/build/anfo-0.98/debian/tmp/usr/include/anfo' /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/elk' /usr/bin/install -c anfo.scm '/build/anfo-0.98/debian/tmp/usr/share/elk' make[4]: Leaving directory '/build/anfo-0.98/src' make[3]: Leaving directory '/build/anfo-0.98/src' make[2]: Leaving directory '/build/anfo-0.98/src' Making install in man make[2]: Entering directory '/build/anfo-0.98/man' make[3]: Entering directory '/build/anfo-0.98/man' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/anfo-0.98/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 '/build/anfo-0.98/debian/tmp/usr/share/man/man1' make[3]: Leaving directory '/build/anfo-0.98/man' make[2]: Leaving directory '/build/anfo-0.98/man' make[2]: Entering directory '/build/anfo-0.98' make[3]: Entering directory '/build/anfo-0.98' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/doc/anfo' /usr/bin/install -c -m 644 README '/build/anfo-0.98/debian/tmp/usr/share/doc/anfo/.' /bin/mkdir -p '/build/anfo-0.98/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 '/build/anfo-0.98/debian/tmp/usr/share/doc/anfo/example' make[3]: Leaving directory '/build/anfo-0.98' make[2]: Leaving directory '/build/anfo-0.98' make[1]: Leaving directory '/build/anfo-0.98' debian/rules override_dh_install make[1]: Entering directory '/build/anfo-0.98' 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. --> libpopt-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 /build/anfo-0.98/debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.so.0 debian/libanfo0/usr/lib/x86_64-linux-gnu mv /build/anfo-0.98/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 '/build/anfo-0.98' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/anfo-0.98' dh_installman # delete unused manpage find debian/anfo -name anfo-sge.1 -delete make[1]: Leaving directory '/build/anfo-0.98' dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/anfo-0.98' dh_fixperms find debian/anfo -perm -5 -type f \( -name '*.scm' \) -print0 2>/dev/null | xargs -0r chmod 644 make[1]: Leaving directory '/build/anfo-0.98' dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libanfo0/usr/lib/x86_64-linux-gnu/libanfo.so.0.0.0 was not linked against libpopt.so.0 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/anfo/usr/bin/anfo debian/anfo/usr/bin/dnaindex debian/anfo/usr/bin/fa2dna debian/anfo/usr/lib/anfo/index-test debian/anfo/usr/bin/anfo-tool debian/anfo/usr/lib/anfo/file-info were not linked against libbz2.so.1.0 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libanfo0' in '../libanfo0_0.98-7_amd64.deb'. dpkg-deb: building package 'libanfo0-dbgsym' in '../libanfo0-dbgsym_0.98-7_amd64.deb'. dpkg-deb: building package 'libanfo0-dev' in '../libanfo0-dev_0.98-7_amd64.deb'. dpkg-deb: building package 'anfo' in '../anfo_0.98-7_amd64.deb'. dpkg-deb: building package 'anfo-dbgsym' in '../anfo-dbgsym_0.98-7_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../anfo_0.98-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/54581 and its subdirectories I: Current time: Wed Jul 7 00:04:47 -12 2021 I: pbuilder-time-stamp: 1625659487