Diff of the two buildlogs: -- --- b1/build.log 2021-07-07 12:04:48.264682256 +0000 +++ b2/build.log 2021-07-07 12:06:15.661396255 +0000 @@ -1,6 +1,6 @@ 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: Current time: Wed Aug 10 08:27:50 +14 2022 +I: pbuilder-time-stamp: 1660069670 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ 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: Signature made Tue Oct 16 04:55:48 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -33,136 +33,170 @@ 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: user script /srv/workspace/pbuilder/36640/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/36640/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/36640/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + 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='> ' + INVOCATION_ID=52c588b6a4fe4b1383ff71373620ed83 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=36640 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' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.JJXvOLF4it/pbuilderrc_eHZA --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.JJXvOLF4it/b2 --logfile b2/build.log anfo_0.98-7.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 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 + Linux i-capture-the-hostname 5.10.0-0.bpo.7-amd64 #1 SMP Debian 5.10.40-1~bpo10+1 (2021-06-04) 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 + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 10 08:27 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 10 04:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/36640/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -291,7 +325,7 @@ 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) +Fetched 26.8 MB in 0s (72.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) @@ -617,7 +651,7 @@ 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 +I: Running cd /build/anfo-0.98/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 @@ -831,7 +865,7 @@ configure: WARNING: unrecognized options: --disable-maintainer-mode checking the archiver (ar) interface... ar dh_auto_build - make -j15 + make -j16 make[1]: Entering directory '/build/anfo-0.98' make all-recursive make[2]: Entering directory '/build/anfo-0.98' @@ -839,41 +873,43 @@ 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.) +[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 -Werror=format-security -c -o concurrent_stream.lo concurrent_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 ducttape.lo ducttape.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 index.lo index.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 misc_streams.lo misc_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 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=. 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-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 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 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 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 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 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 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 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 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 util.cc -fPIC -DPIC -o .libs/util.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -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: 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: 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 +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 In file included from stream.h:20, from misc_streams.h:4, from misc_streams.cc:5: @@ -969,7 +1005,6 @@ /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: @@ -987,305 +1022,339 @@ /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] +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.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 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 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.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 misc_streams.cc:5: -stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] +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.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 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 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.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 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 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.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 misc_streams.cc:5: -stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] +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 compress_stream.h:22, - from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 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 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 compress_stream.h:22, - from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 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 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 compress_stream.h:22, - from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 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 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 compress_stream.h:22, - from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 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 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 compress_stream.h:22, - from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 misc_streams.h:4, - from misc_streams.cc:5: -stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] +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 stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 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 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 stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 misc_streams.h:4, - from misc_streams.cc:5: -stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] +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 stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 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 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 stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 misc_streams.h:4, - from misc_streams.cc:5: -stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] +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 +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 compress_stream.h:22, - from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 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 ) ; - ^~~~~~~~ +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: + 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 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 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 compress_stream.h:22, - from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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 align.cc:21: + 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 /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: + 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 align.h:22, - from align.cc:21: + 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 /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: + 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 align.h:22, - from align.cc:21: + 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 align.h:22, - from align.cc:21: + 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 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_ ; @@ -1295,14 +1364,14 @@ 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: + 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 align.cc:21: + 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 ) ^~~~~~~~ @@ -1311,14 +1380,14 @@ 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: + 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 align.cc:21: + 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 ) ; @@ -1333,67 +1402,45 @@ 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: + 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.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: +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 /usr/include/google/protobuf/io/zero_copy_stream.h:111, - from compress_stream.h:22, - from stream.cc:21: + 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.cc:21: +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 /usr/include/google/protobuf/io/zero_copy_stream.h:111, - from compress_stream.h:22, - from stream.cc:21: + 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.cc:21: +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 ) ; @@ -1405,16 +1452,16 @@ ^~~~~~~~ In file included from /usr/include/c++/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: + 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; ^~~~~~~~ +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 align.h:22, - from anfo_common.h:22, - from anfo_common.cc:21: + 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_ ; ^~~~~~~~ @@ -1422,17 +1469,12 @@ 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: + 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 align.h:22, - from anfo_common.h:22, - from anfo_common.cc:21: + 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 ) ^~~~~~~~ @@ -1440,177 +1482,181 @@ 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: + 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 align.h:22, - from anfo_common.h:22, - from anfo_common.cc:21: + 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 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] +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 align_fwd.h:5, - from align.h:20, - from align.cc:21: + 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 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 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 align_fwd.h:5, - from align.h:20, - from align.cc:21: + 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 align.h:22, - from align.cc:21: -stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] +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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: + 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 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] +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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo_common.cc:21: + 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 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 ) - ^~~~~~~~ + 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 align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo_common.cc:21: + 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 align.h:22, - from align.cc:21: +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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: + 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 align.h:22, - from align.cc:21: +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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: + 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 align.h:22, - from align.cc:21: +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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: + 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 align.h:22, - from align.cc:21: +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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: + 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 align.h:22, - from align.cc:21: +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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: + 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; ^~~~~~~~ @@ -1618,15 +1664,9 @@ 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( - ^~~~~~~~ +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, @@ -1638,23 +1678,69 @@ /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 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 misc_streams.h:4, - from misc_streams.cc:5: + 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 align.h:22, - from align.cc:21: -stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] +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 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 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, @@ -1663,133 +1749,175 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from align.cc:21: + 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: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 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 align.cc:21: + 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: +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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: + 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 align.h:22, - from align.cc:21: +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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: + 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 align.h:22, - from align.cc:21: +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 +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; + ^~~~~~~~ +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: + 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: +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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: + 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 align.h:22, - from align.cc:21: +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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: + 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 align.h:22, - from align.cc:21: +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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: + 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 align.h:22, - from align.cc:21: +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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: + 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; ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo_common.cc:21: + 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_ ; @@ -1801,13 +1929,13 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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_common.cc:21: + 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 ) ; ^~~~~~~~ @@ -1818,16 +1946,37 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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 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 align.h:22, from anfo_common.h:22, - from anfo_common.cc:21: + 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 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, @@ -1835,13 +1984,52 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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 /usr/include/c++/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; + ^~~~~~~~ +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 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 align.h:22, from anfo_common.h:22, - from anfo_common.cc:21: + 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 ^~~~~~~~ @@ -1852,13 +2040,28 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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 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 align.h:22, from anfo_common.h:22, - from anfo_common.cc:21: + 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 ^~~~~~~~ @@ -1869,13 +2072,28 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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 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 align.h:22, from anfo_common.h:22, - from anfo_common.cc:21: + 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_ ; ^~~~~~~~ @@ -1886,13 +2104,13 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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_common.cc:21: + 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 ^~~~~~~~ @@ -1903,13 +2121,13 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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_common.cc:21: + 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 ) ; ^~~~~~~~ @@ -1920,13 +2138,58 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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 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 align.h:22, from anfo_common.h:22, - from anfo_common.cc:21: + 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_ ; ^~~~~~~~ @@ -1937,13 +2200,13 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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_common.cc:21: + 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 ) : ^~~~~~~~ @@ -1954,13 +2217,74 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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 align.h:22, from anfo_common.h:22, - from anfo_common.cc:21: + 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_ ; ^~~~~~~~ @@ -1971,13 +2295,13 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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_common.cc:21: + 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 ) : ^~~~~~~~ @@ -1988,13 +2312,13 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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_common.cc:21: + 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_ ; ^~~~~~~~ @@ -2005,13 +2329,13 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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_common.cc:21: + 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 ) : ^~~~~~~~ @@ -2022,13 +2346,13 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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_common.cc:21: + 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_ ; ^~~~~~~~ @@ -2039,13 +2363,13 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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_common.cc:21: + 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 ) ; ^~~~~~~~ @@ -2056,16 +2380,36 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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 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 align.h:22, from anfo_common.h:22, - from anfo_common.cc:21: + 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 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, @@ -2073,32 +2417,25 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: + 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 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: + 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 ducttape.h:21, +In file included 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 ) - ^~~~~~~~ +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, @@ -2109,19 +2446,9 @@ /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, +In file included 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] +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, @@ -2134,12 +2461,11 @@ /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, +In file included 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 ) - ^~~~~~~~ +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, @@ -2150,18 +2476,11 @@ /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, +In file included 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( - ^~~~~~~~ +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, @@ -2172,299 +2491,239 @@ /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] +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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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-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 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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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-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] +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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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-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 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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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 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 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 sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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 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 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 sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + 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 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 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 sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + 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 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 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 sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + 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 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 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 sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + 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 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 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 sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + 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 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 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 sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + 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 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 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 sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + 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 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 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 sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + 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 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 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 config.pb.h:9, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + 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 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 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 config.pb.h:9, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + 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 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] +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 config.pb.h:9, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + 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 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 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 config.pb.h:9, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + 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; ^~~~~~~~ @@ -2498,6 +2757,21 @@ /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; + ^~~~~~~~ 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] @@ -2528,27 +2802,6 @@ /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] @@ -2624,6 +2877,84 @@ /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 ducttape.cc:21: ducttape.h:139:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr< std::ostream > out_ ; @@ -2638,9 +2969,20 @@ /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: +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 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_ ; @@ -2649,16 +2991,11 @@ 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: + 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 align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: +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 ) ; ^~~~~~~~ @@ -2666,16 +3003,11 @@ 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: + 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 align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: +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_ ; ^~~~~~~~ @@ -2683,16 +3015,11 @@ 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: + 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 align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: +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 ^~~~~~~~ @@ -2700,16 +3027,11 @@ 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: + 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 align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: +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 ^~~~~~~~ @@ -2717,16 +3039,11 @@ 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: + 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 align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: +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_ ; ^~~~~~~~ @@ -2734,16 +3051,11 @@ 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: + 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 align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: +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 ^~~~~~~~ @@ -2751,16 +3063,11 @@ 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: + 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 align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: +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 ) ; ^~~~~~~~ @@ -2768,17 +3075,15 @@ 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: + 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 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] + 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, @@ -2788,16 +3093,16 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + 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-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 ) : - ^~~~~~~~ + 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, @@ -2805,14 +3110,14 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + 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-elk.cc:27: -stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 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, @@ -2822,16 +3127,16 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + 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-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 ) : - ^~~~~~~~ + 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, @@ -2839,15 +3144,15 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + 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-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_ ; + 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, @@ -2856,16 +3161,16 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + 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-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 ) : - ^~~~~~~~ + 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, @@ -2873,15 +3178,15 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + 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-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_ ; + 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, @@ -2890,16 +3195,16 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + 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-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 ) ; - ^~~~~~~~ + 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, @@ -2907,24 +3212,31 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + 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-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 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 align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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; ^~~~~~~~ @@ -2985,6 +3297,54 @@ /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 output_streams.h:21, from output_streams.cc:21: stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] @@ -2999,6 +3359,64 @@ /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 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 output_streams.h:21, from output_streams.cc:21: stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] @@ -3041,6 +3459,137 @@ /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; + ^~~~~~~~ +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 output_streams.h:21, from output_streams.cc:21: stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] @@ -3245,10 +3794,10 @@ /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 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, @@ -3260,610 +3809,100 @@ /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 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 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: + 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 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 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 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: + 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 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 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 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: + 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 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 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 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: + 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 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 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 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: + 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; ^~~~~~~~ -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_ ] ) ; +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 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: + 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 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 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, @@ -3871,29 +3910,40 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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 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 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 anfo_common.h:22, - from anfo-elk.cc:27: + 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 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 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, @@ -3901,38 +3951,45 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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 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 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 anfo_common.h:22, - from anfo-elk.cc:27: + 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 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 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 anfo_common.h:22, - from anfo-elk.cc:27: + from align.cc:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ @@ -3958,7 +4015,8 @@ /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ -In file included from sequence.cc:23: +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_ ; @@ -3967,11 +4025,14 @@ 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: + 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 sequence.cc:23: +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 ) ; ^~~~~~~~ @@ -3979,11 +4040,14 @@ 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: + 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 sequence.cc:23: +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_ ; ^~~~~~~~ @@ -3991,11 +4055,14 @@ 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: + 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 sequence.cc:23: +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 ^~~~~~~~ @@ -4003,11 +4070,14 @@ 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: + 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 sequence.cc:23: +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 ^~~~~~~~ @@ -4015,11 +4085,14 @@ 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: + 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 sequence.cc:23: +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_ ; ^~~~~~~~ @@ -4027,11 +4100,14 @@ 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: + 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 sequence.cc:23: +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 ^~~~~~~~ @@ -4039,11 +4115,14 @@ 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: + 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 sequence.cc:23: +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 ) ; ^~~~~~~~ @@ -4051,7 +4130,9 @@ 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: + 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; ^~~~~~~~ @@ -4134,19 +4215,8 @@ /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: +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_ ; ^~~~~~~~ @@ -4154,11 +4224,14 @@ 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: + 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 sequence.cc:23: +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 ) : ^~~~~~~~ @@ -4166,11 +4239,14 @@ 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: + 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 sequence.cc:23: +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_ ; ^~~~~~~~ @@ -4178,11 +4254,14 @@ 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: + 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 sequence.cc:23: +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 ) : ^~~~~~~~ @@ -4190,11 +4269,26 @@ 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: + 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 sequence.cc:23: +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 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_ ; ^~~~~~~~ @@ -4202,11 +4296,14 @@ 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: + 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 sequence.cc:23: +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 ) : ^~~~~~~~ @@ -4214,11 +4311,14 @@ 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: + 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 sequence.cc:23: +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_ ; ^~~~~~~~ @@ -4226,11 +4326,14 @@ 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: + 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 sequence.cc:23: +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 ) ; ^~~~~~~~ @@ -4238,11 +4341,14 @@ 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: + 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 sequence.cc:23: +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_ ; ^~~~~~~~ @@ -4250,88 +4356,12 @@ 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: + 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; ^~~~~~~~ -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: @@ -4566,7 +4596,6 @@ /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_ ; @@ -4639,7 +4668,10 @@ /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 +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.o anfo.cc +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 +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 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_ ; @@ -4713,8 +4745,214 @@ /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 +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 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 +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 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; + ^~~~~~~~ In file included from stream.h:20, from align.h:22, from anfo_common.h:22, @@ -4821,7 +5059,7 @@ /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 +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 align.h:22, from anfo_common.h:22, from anfo.cc:21: @@ -5112,215 +5350,9 @@ /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 ducttape.cc -o ducttape.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -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: @@ -5628,10 +5660,12 @@ /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 anfo_common.cc -o anfo_common.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -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 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 +/bin/sh ../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") @@ -5639,17 +5673,17 @@ 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 +/bin/sh ../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/sh ../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/sh ../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/sh ../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/sh ../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/sh ../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/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/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/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/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' @@ -5662,7 +5696,7 @@ 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 -j16 check VERBOSE=1 make[1]: Entering directory '/build/anfo-0.98' Making check in src make[2]: Entering directory '/build/anfo-0.98/src' @@ -5692,7 +5726,7 @@ 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' + /bin/sh ../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; }; }) @@ -5702,7 +5736,7 @@ 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' + /bin/sh ../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' @@ -5712,7 +5746,7 @@ 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' + /bin/sh ../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' @@ -5797,28 +5831,30 @@ 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) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/anfo/usr/bin/anfo debian/anfo/usr/lib/anfo/index-test debian/anfo/usr/bin/fa2dna debian/anfo/usr/lib/anfo/file-info debian/anfo/usr/bin/dnaindex debian/anfo/usr/bin/anfo-tool 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 'anfo-dbgsym' in '../anfo-dbgsym_0.98-7_amd64.deb'. +dpkg-deb: building package 'anfo' in '../anfo_0.98-7_amd64.deb'. dpkg-deb: building package 'libanfo0-dbgsym' in '../libanfo0-dbgsym_0.98-7_amd64.deb'. +dpkg-deb: building package 'libanfo0' in '../libanfo0_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: user script /srv/workspace/pbuilder/36640/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/36640/tmp/hooks/B01_cleanup finished 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 +I: removing directory /srv/workspace/pbuilder/36640 and its subdirectories +I: Current time: Wed Aug 10 08:29:15 +14 2022 +I: pbuilder-time-stamp: 1660069755