Diff of the two buildlogs: -- --- b1/build.log 2024-07-29 18:03:16.410964158 +0000 +++ b2/build.log 2024-07-29 18:07:39.431786564 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Aug 31 12:24:57 -12 2025 -I: pbuilder-time-stamp: 1756686297 +I: Current time: Tue Jul 30 08:03:19 +14 2024 +I: pbuilder-time-stamp: 1722276199 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./anfo_0.98-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.Dfa3u7Wp/trustedkeys.kbx': General error -gpgv: Signature made Wed Nov 25 07:08:08 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.eYtoMjVw/trustedkeys.kbx': General error +gpgv: Signature made Thu Nov 26 09:08:08 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -34,135 +34,166 @@ dpkg-source: info: applying 05-autoreconf.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4031259/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1543234/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 30 08:03 /bin/sh -> /bin/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/1543234/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1543234/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - 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,-fixfilepath parallel=42 ' - DISTRIBUTION='bullseye' - 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]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build/reproducible-path + 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,-fixfilepath parallel=20 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='7329331bf6f445d7ba4430d281735d48' - 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='4031259' - PS1='# ' - PS2='> ' + INVOCATION_ID=47bde9f6887748559eb3872a5c10b65a + 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=1543234 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/r-b-build.FtISkZTb/pbuilderrc_jXOW --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FtISkZTb/b1 --logfile b1/build.log anfo_0.98-8.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://213.165.73.152:3128' + 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/r-b-build.FtISkZTb/pbuilderrc_EW2d --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FtISkZTb/b2 --logfile b2/build.log anfo_0.98-8.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://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.9.7+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1~bpo12+1 (2024-07-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-23-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.99-1 (2024-07-15) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Mar 27 2024 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Mar 27 2024 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Mar 27 2024 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Mar 27 2024 more - -rwsr-xr-x 1 root root 55528 Mar 27 2024 mount - -rwxr-xr-x 1 root root 18664 Mar 27 2024 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 9 03:46 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Mar 27 2024 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Jan 19 2024 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Mar 27 2024 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Mar 27 2024 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/4031259/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Mar 29 00:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 69032 Mar 29 00:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Mar 29 00:09 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Mar 29 00:09 more + -rwsr-xr-x 1 root root 55528 Mar 29 00:09 mount + -rwxr-xr-x 1 root root 18664 Mar 29 00:09 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Jul 30 08:03 sh -> /bin/bash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Mar 29 00:09 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Jan 20 2024 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Mar 29 00:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Mar 29 00:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/1543234/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -290,7 +321,7 @@ Get: 72 http://deb.debian.org/debian bullseye/main amd64 libprotoc23 amd64 3.12.4-1+deb11u1 [802 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 protobuf-compiler amd64 3.12.4-1+deb11u1 [75.3 kB] -Fetched 28.4 MB in 0s (68.9 MB/s) +Fetched 28.4 MB in 1s (43.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19711 files and directories currently installed.) @@ -605,7 +636,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/anfo-0.98/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../anfo_0.98-8_source.changes +I: user script /srv/workspace/pbuilder/1543234/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/1543234/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../anfo_0.98-8_source.changes dpkg-buildpackage: info: source package anfo dpkg-buildpackage: info: source version 0.98-8 dpkg-buildpackage: info: source distribution unstable @@ -844,7 +879,7 @@ config.status: executing libtool commands checking the archiver (ar) interface... ar dh_auto_build - make -j42 + make -j20 make[1]: Entering directory '/build/reproducible-path/anfo-0.98' make all-recursive make[2]: Entering directory '/build/reproducible-path/anfo-0.98' @@ -858,42 +893,42 @@ make all-am make[4]: Entering directory '/build/reproducible-path/anfo-0.98/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 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output.pb.cc g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dnaindex.o dnaindex.cc g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo-tool.o anfo-tool.cc g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o index-test.o index-test.cc g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 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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: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo-elk.cc -fPIC -DPIC -o .libs/anfo-elk.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c config.pb.cc -fPIC -DPIC -o .libs/config.pb.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c fastlz.c -o fastlz.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 In file included from anfo-tool.cc:21: compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; @@ -918,36 +953,12 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from index-test.cc:27: -compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ In file included from anfo-tool.cc:21: compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] 198 | else if( r != Z_OK ) throw zs_.msg ; | ^~~~~~~~~~~~~ compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' -In file included from index-test.cc:27: -compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ 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] @@ -973,31 +984,12 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from index-test.cc:27: -compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': -compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 198 | else if( r != Z_OK ) throw zs_.msg ; - | ^~~~~~~~~~~~~ -compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' In file included from anfo-tool.cc:21: compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] 379 | else if( r < BZ_OK ) throw BzipError( r ) ; | ^~~~~~~~~~~~~~~~~~~~ compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept' -In file included from index-test.cc:27: -compress_stream.h: At global scope: -compress_stream.h:225:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | 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] 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( @@ -1010,43 +1002,6 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from index-test.cc:27: -compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from index-test.cc:27: -compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': -compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 379 | else if( r < BZ_OK ) throw BzipError( r ) ; - | ^~~~~~~~~~~~~~~~~~~~ -compress_stream.h:379:26: 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] - 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: -compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)': -compress_stream.h:395:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( - | ^~~~~~~~ In file included from stream.cc:21: compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; @@ -1055,16 +1010,6 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; @@ -1131,48 +1076,65 @@ 57 | template class auto_ptr; | ^~~~~~~~ In file included from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + from concurrent_stream.h:23, + from concurrent_stream.cc:1: +compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)': +compress_stream.h:395:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from stream.h:20, + from concurrent_stream.h:23, + from concurrent_stream.cc:1: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | 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] 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + from ducttape.h:21, + from ducttape.cc:21: compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + from ducttape.h:21, + from ducttape.cc:21: compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] 198 | else if( r != Z_OK ) throw zs_.msg ; | ^~~~~~~~~~~~~ compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' In file included from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + 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] 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; @@ -1180,32 +1142,32 @@ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + from ducttape.h:21, + from ducttape.cc:21: compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + from ducttape.h:21, + from ducttape.cc:21: compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] 379 | else if( r < BZ_OK ) throw BzipError( r ) ; @@ -1218,45 +1180,18 @@ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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] - 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from sequence.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | 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] - 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from sequence.cc:21: + from align_fwd.h:5, + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +stream.h: At global scope: +stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -1268,12 +1203,11 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) - | ^~~~~~~~ +stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -1284,54 +1218,40 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 198 | else if( r != Z_OK ) throw zs_.msg ; - | ^~~~~~~~~~~~~ -compress_stream.h:198:26: 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] - 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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] + 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from sequence.cc:21: + from align_fwd.h:5, + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) - | ^~~~~~~~ +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] + 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from sequence.cc:21: + from align_fwd.h:5, + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 198 | else if( r != Z_OK ) throw zs_.msg ; - | ^~~~~~~~~~~~~ -compress_stream.h:198:26: 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] - 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -1343,12 +1263,11 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) - | ^~~~~~~~ +stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -1359,118 +1278,86 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 379 | else if( r < BZ_OK ) throw BzipError( r ) ; - | ^~~~~~~~~~~~~~~~~~~~ -compress_stream.h:379:26: 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:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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] + 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) +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] + 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo_common.cc:21: -compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from ducttape.h:21, + from ducttape.cc:21: +stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ -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] - 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( - | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from sequence.cc:21: + from align_fwd.h:5, + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +In file included from ducttape.h:21, + from ducttape.cc:21: +stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo_common.cc:21: + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) - | ^~~~~~~~ +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] + 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo_common.cc:21: + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 379 | else if( r < BZ_OK ) throw BzipError( r ) ; - | ^~~~~~~~~~~~~~~~~~~~ -compress_stream.h:379:26: 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: In destructor 'virtual DeflateStream::~DeflateStream()': -compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 198 | else if( r != Z_OK ) throw zs_.msg ; - | ^~~~~~~~~~~~~ -compress_stream.h:198:26: 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] - 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( - | ^~~~~~~~ +stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -1481,186 +1368,126 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 198 | else if( r != Z_OK ) throw zs_.msg ; - | ^~~~~~~~~~~~~ -compress_stream.h:198:26: 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] - 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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] + 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) - | ^~~~~~~~ +In file included from ducttape.h:21, + from ducttape.cc:21: +stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from ducttape.h:21, + from ducttape.cc:21: +stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo_common.cc:21: + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) - | ^~~~~~~~ +In file included from ducttape.h:21, + from ducttape.cc:21: +stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo_common.cc:21: + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 379 | else if( r < BZ_OK ) throw BzipError( r ) ; - | ^~~~~~~~~~~~~~~~~~~~ -compress_stream.h:379:26: 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] - 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( - | ^~~~~~~~ +In file included from ducttape.h:21, + from ducttape.cc:21: +stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo_common.cc:21: -compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': -compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 379 | else if( r < BZ_OK ) throw BzipError( r ) ; - | ^~~~~~~~~~~~~~~~~~~~ -compress_stream.h:379:26: 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] - 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( - | ^~~~~~~~ +In file included from ducttape.cc:21: +ducttape.h:139:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 139 | std::auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo_common.cc:21: + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: +In file included from index-test.cc:27: compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: +In file included from index-test.cc:27: compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: +In file included from index-test.cc:27: compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] 198 | else if( r != Z_OK ) throw zs_.msg ; | ^~~~~~~~~~~~~ compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: +In file included from index-test.cc:27: compress_stream.h: At global scope: compress_stream.h:225:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; @@ -1668,36 +1495,24 @@ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: +In file included from index-test.cc:27: compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: +In file included from index-test.cc:27: compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] 379 | else if( r < BZ_OK ) throw BzipError( r ) ; @@ -1710,11 +1525,8 @@ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ @@ -1771,38 +1583,6 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | 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] - 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ In file included from ducttape.h:21, from anfo-tool.cc:22: stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] @@ -1855,194 +1635,150 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 198 | else if( r != Z_OK ) throw zs_.msg ; - | ^~~~~~~~~~~~~ -compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' -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] - 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from ducttape.h:21, + from anfo-tool.cc:22: +stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +In file included from ducttape.h:21, + from anfo-tool.cc:22: +stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from ducttape.h:21, + from anfo-tool.cc:22: +stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -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] - 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ +In file included from ducttape.h:21, + from anfo-tool.cc:22: +stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) - | ^~~~~~~~ +In file included from ducttape.h:21, + from anfo-tool.cc:22: +stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output - | ^~~~~~~~ +In file included from ducttape.h:21, + from anfo-tool.cc:22: +stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer +In file included from ducttape.h:21, + from anfo-tool.cc:22: +stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 379 | else if( r < BZ_OK ) throw BzipError( r ) ; - | ^~~~~~~~~~~~~~~~~~~~ -compress_stream.h:379:26: 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] - 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( - | ^~~~~~~~ +In file included from ducttape.h:21, + from anfo-tool.cc:22: +stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from ducttape.h:21, + from anfo-tool.cc:22: +stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer +In file included from anfo-tool.cc:22: +ducttape.h:139:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 139 | std::auto_ptr< std::ostream > out_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +In file included from anfo-tool.cc:24: +output_streams.h:45:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 45 | auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: -stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from anfo-tool.cc:24: +output_streams.h:72:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 72 | std::auto_ptr< std::ostream > out_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -2052,11 +1788,10 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: -stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : - | ^~~~~~~~ +In file included from anfo-tool.cc:24: +output_streams.h:123:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 123 | std::auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -2065,10 +1800,9 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: -stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from anfo-tool.cc:24: +output_streams.h:138:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 138 | std::auto_ptr< std::ostream > out_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -2078,11 +1812,10 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: -stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : - | ^~~~~~~~ +In file included from anfo-tool.cc:24: +output_streams.h:149:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 149 | std::auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -2091,8 +1824,127 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: +In file included from anfo-tool.cc:24: +output_streams.h:176:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 176 | std::auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from anfo-tool.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': +compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 198 | else if( r != Z_OK ) throw zs_.msg ; + | ^~~~~~~~~~~~~ +compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +compress_stream.h: At global scope: +compress_stream.h:225:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': +compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 379 | else if( r < BZ_OK ) throw BzipError( r ) ; + | ^~~~~~~~~~~~~~~~~~~~ +compress_stream.h:379:26: 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] + 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: stream.h: At global scope: stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; @@ -2100,201 +1952,291 @@ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: -stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: -stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : - | ^~~~~~~~ +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: -stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: -stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; - | ^~~~~~~~ +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from concurrent_stream.h:23, - from concurrent_stream.cc:1: +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from concurrent_stream.h:23, - from concurrent_stream.cc:1: +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: -stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer - | ^~~~~~~~ +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +stream.h: At global scope: +stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -2308,9 +2250,9 @@ | ^~~~~~~~ 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] - 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : - | ^~~~~~~~ +stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -2323,8 +2265,8 @@ | ^~~~~~~~ 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] - 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -2338,9 +2280,9 @@ | ^~~~~~~~ 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] - 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : - | ^~~~~~~~ +stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -2353,8 +2295,8 @@ | ^~~~~~~~ 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] - 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -2368,9 +2310,9 @@ | ^~~~~~~~ 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] - 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; - | ^~~~~~~~ +stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -2383,8 +2325,8 @@ | ^~~~~~~~ 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] - 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; +stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -2396,20 +2338,23 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-tool.cc:22: -ducttape.h:139:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 139 | std::auto_ptr< std::ostream > out_ ; - | ^~~~~~~~ +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] + 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from anfo-tool.cc:21: + from stream.h:20, + from concurrent_stream.h:23, + from concurrent_stream.cc:1: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: +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] 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -2417,12 +2362,14 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from stream.h:20, + from concurrent_stream.h:23, + from concurrent_stream.cc:1: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: +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] 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : | ^~~~~~~~ @@ -2430,12 +2377,14 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from stream.h:20, + from concurrent_stream.h:23, + from concurrent_stream.cc:1: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: +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] 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -2443,12 +2392,14 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from stream.h:20, + from concurrent_stream.h:23, + from concurrent_stream.cc:1: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: +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] 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : | ^~~~~~~~ @@ -2456,26 +2407,14 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | 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] - 178 | auto_ptr< Result > r( outgoing_[ next_out_++ ] ) ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: +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] 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -2483,12 +2422,14 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from stream.h:20, + from concurrent_stream.h:23, + from concurrent_stream.cc:1: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: +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] 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : | ^~~~~~~~ @@ -2496,26 +2437,14 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | 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] - 212 | auto_ptr< Result > r( incoming_[ next_in_ ] ) ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: +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] 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -2523,12 +2452,14 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from stream.h:20, + from concurrent_stream.h:23, + from concurrent_stream.cc:1: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: +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] 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; | ^~~~~~~~ @@ -2536,12 +2467,14 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from stream.h:20, + from concurrent_stream.h:23, + from concurrent_stream.cc:1: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: +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] 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; | ^~~~~~~~ @@ -2549,77 +2482,103 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from stream.h:20, + from concurrent_stream.h:23, + from concurrent_stream.cc:1: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -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] - 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: +compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from index-test.cc:27: + from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +In file included from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: +compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from index-test.cc:27: + from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ +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] + 178 | auto_ptr< Result > r( outgoing_[ next_out_++ ] ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from index-test.cc:27: + from stream.h:20, + from concurrent_stream.h:23, + from concurrent_stream.cc:1: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output - | ^~~~~~~~ +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] + 212 | auto_ptr< Result > r( incoming_[ next_in_ ] ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from index-test.cc:27: + from stream.h:20, + from concurrent_stream.h:23, + from concurrent_stream.cc:1: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer +In file included from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: +compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': +compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 198 | else if( r != Z_OK ) throw zs_.msg ; + | ^~~~~~~~~~~~~ +compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' +In file included from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: +compress_stream.h: At global scope: +compress_stream.h:225:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from index-test.cc:27: + from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, +In file included from stream.h:20, + 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] - 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ +compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -2630,11 +2589,18 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, +In file included from stream.h:20, + from misc_streams.h:4, from misc_streams.cc:5: -stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': +compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 379 | else if( r < BZ_OK ) throw BzipError( r ) ; + | ^~~~~~~~~~~~~~~~~~~~ +compress_stream.h:379:26: 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] + 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -2645,63 +2611,107 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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] + 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer - | ^~~~~~~~ +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] + 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 198 | else if( r != Z_OK ) throw zs_.msg ; + | ^~~~~~~~~~~~~ +compress_stream.h:198:26: 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] + 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ -In file included from index-test.cc:30: -stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] + 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, +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:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 379 | else if( r < BZ_OK ) throw BzipError( r ) ; + | ^~~~~~~~~~~~~~~~~~~~ +compress_stream.h:379:26: 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] + 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | 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: -stream.h: At global scope: -stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -2714,12 +2724,13 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, +In file included from stream.h:20, + from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: -stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -2731,27 +2742,41 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output +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:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 198 | else if( r != Z_OK ) throw zs_.msg ; + | ^~~~~~~~~~~~~ +compress_stream.h:198:26: 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] + 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, +In file included from stream.h:20, + from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: -stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ +compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -2763,12 +2788,19 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, +In file included from stream.h:20, + from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: -stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output - | ^~~~~~~~ +compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': +compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 379 | else if( r < BZ_OK ) throw BzipError( r ) ; + | ^~~~~~~~~~~~~~~~~~~~ +compress_stream.h:379:26: 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] + 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -2780,128 +2812,460 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: +In file included from output_streams.h:21, + from output_streams.cc:21: stream.h: At global scope: stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from sequence.cc:21: + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: +In file included from output_streams.h:21, + from output_streams.cc:21: stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; | ^~~~~~~~ -In file included from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h: At global scope: -stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.h:21, + from output_streams.cc:21: +stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from sequence.cc:21: + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.h:21, + from output_streams.cc:21: +stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | 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] + 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | 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] + 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.h:21, + from output_streams.cc:21: +stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.h:21, + from output_streams.cc:21: +stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | 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] + 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.h:21, + from output_streams.cc:21: +stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.h:21, + from output_streams.cc:21: +stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.h:21, + from output_streams.cc:21: +stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.h:21, + from output_streams.cc:21: +stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.h:21, + from output_streams.cc:21: +stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.h:21, + from output_streams.cc:21: +stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.h:21, + from output_streams.cc:21: +stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.h:21, + from output_streams.cc:21: +stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.cc:21: +output_streams.h:45:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 45 | auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.cc:21: +output_streams.h:72:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 72 | std::auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.cc:21: +output_streams.h:123:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 123 | std::auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.cc:21: +output_streams.h:138:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 138 | std::auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.cc:21: +output_streams.h:149:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 149 | std::auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.cc:21: +output_streams.h:176:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 176 | std::auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +In file included from stream.h:20, + from align.h:22, + from align.cc:21: +compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +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] + 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: -stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 198 | else if( r != Z_OK ) throw zs_.msg ; + | ^~~~~~~~~~~~~ +compress_stream.h:198:26: 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] + 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from sequence.cc:21: + from align_fwd.h:5, + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ +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] + 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: +stream.h: At global scope: +stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: -stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output - | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output - | ^~~~~~~~ + from anfo_common.cc:21: +stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from sequence.cc:21: + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: +stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -2909,38 +3273,46 @@ 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: +stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +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:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 379 | else if( r < BZ_OK ) throw BzipError( r ) ; + | ^~~~~~~~~~~~~~~~~~~~ +compress_stream.h:379:26: 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] + 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ @@ -2961,72 +3333,81 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer | ^~~~~~~~ -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] - 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: +stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c util.cc -o util.o >/dev/null 2>&1 +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] + 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: -stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ +stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -3041,8 +3422,8 @@ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: -stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer +stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -3058,9 +3439,9 @@ In file included from align.h:22, from anfo_common.h:22, from anfo_common.cc:21: -stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -3072,27 +3453,29 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output +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] + 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer - | ^~~~~~~~ + from anfo_common.cc:21: +stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -3100,28 +3483,33 @@ 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: -stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer +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] + 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from sequence.cc:21: + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ + from anfo_common.cc:21: +stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -3129,15 +3517,15 @@ 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer + from anfo_common.cc:21: +stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -3146,65 +3534,73 @@ 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: -stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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] + 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from sequence.cc:21: + from align_fwd.h:5, + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: -stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer - | ^~~~~~~~ +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] + 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from sequence.cc:21: + from align_fwd.h:5, + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ + from align.cc:21: +stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: -stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +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] + 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from sequence.cc:21: + from align_fwd.h:5, + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from ducttape.cc:21: +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] 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer | ^~~~~~~~ @@ -3213,13 +3609,39 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from ducttape.cc:21: +In file included from anfo-tool.cc:23: +misc_streams.h: In instantiation of 'void streams::SortingStream::put_result(const output::Result&) [with Comp = streams::by_seqid]': +misc_streams.h:282:16: required from here +misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] + 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +In file included from output.pb.h:31, + from sequence.h:32, + from align_fwd.h:5, + from ducttape.h:20, + from anfo-tool.cc:22: +/usr/include/google/protobuf/message.h:299:7: note: declared here + 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } + | ^~~~~~~~~ +In file included from anfo-tool.cc:23: +misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] + 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +In file included from output.pb.h:31, + from sequence.h:32, + from align_fwd.h:5, + from ducttape.h:20, + from anfo-tool.cc:22: +/usr/include/google/protobuf/message.h:299:7: note: declared here + 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } + | ^~~~~~~~~ +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] 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -3228,13 +3650,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from ducttape.cc:21: +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] 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer | ^~~~~~~~ @@ -3243,13 +3665,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from ducttape.cc:21: +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] 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; | ^~~~~~~~ @@ -3258,17 +3680,43 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, +In file included from anfo-tool.cc:23: +misc_streams.h: In instantiation of 'void streams::SortingStream::put_result(const output::Result&) [with Comp = streams::by_genome_coordinate]': +misc_streams.h:282:16: required from here +misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] + 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +In file included from output.pb.h:31, + from sequence.h:32, + from align_fwd.h:5, + from ducttape.h:20, + from anfo-tool.cc:22: +/usr/include/google/protobuf/message.h:299:7: note: declared here + 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } + | ^~~~~~~~~ +In file included from anfo-tool.cc:23: +misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] + 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +In file included from output.pb.h:31, + from sequence.h:32, + from align_fwd.h:5, + from ducttape.h:20, + from anfo-tool.cc:22: +/usr/include/google/protobuf/message.h:299:7: note: declared here + 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } + | ^~~~~~~~~ +In file included from stream.h:20, + from align.h:22, from anfo_common.h:22, - from anfo.cc:21: -stream.h: At global scope: -stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + from anfo-elk.cc:27: +compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -3277,16 +3725,17 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, +In file included from stream.h:20, + from align.h:22, from anfo_common.h:22, - from anfo.cc:21: -stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ + from anfo-elk.cc:27: +compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -3294,15 +3743,26 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, +In file included from stream.h:20, + from align.h:22, from anfo_common.h:22, - from anfo.cc:21: -stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + from anfo-elk.cc:27: +compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': +compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 198 | else if( r != Z_OK ) throw zs_.msg ; + | ^~~~~~~~~~~~~ +compress_stream.h:198:26: 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] + 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -3311,40 +3771,41 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | 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] - 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 762 | 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:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: + 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, +In file included from stream.h:20, + from align.h:22, from anfo_common.h:22, - from anfo.cc:21: -stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output - | ^~~~~~~~ + from anfo-elk.cc:27: +compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': +compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 379 | else if( r < BZ_OK ) throw BzipError( r ) ; + | ^~~~~~~~~~~~~~~~~~~~ +compress_stream.h:379:26: 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] + 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -3352,39 +3813,44 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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] + 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : - | ^~~~~~~~ +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] + 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: -stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer + from align.cc:21: +stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -3392,33 +3858,29 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: -stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ + from align.cc:21: +stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: -stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer + from align.cc:21: +stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -3426,272 +3888,229 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: -stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ + from align.cc:21: +stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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] + 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : +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] + 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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] + 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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 align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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] + 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from index-test.cc:27: + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : - | ^~~~~~~~ + from stream.cc:22: +stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; - | ^~~~~~~~ +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] + 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from index-test.cc:27: + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; +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] + 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from index-test.cc:27: + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 747 | 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] + 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : - | ^~~~~~~~ +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] + 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + from stream.cc:22: +stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : - | ^~~~~~~~ + from stream.cc:22: +stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: +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] 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from sequence.cc:21: + from compress_stream.h:22, + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: +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] 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from sequence.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from ducttape.h:21, - from ducttape.cc:21: -stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from ducttape.cc:21: -stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : - | ^~~~~~~~ -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:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from misc_streams.h:4, - from misc_streams.cc:5: + from stream.cc:22: stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -3699,14 +4118,12 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from misc_streams.h:4, - from misc_streams.cc:5: + from stream.cc:22: stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : | ^~~~~~~~ @@ -3714,48 +4131,12 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | 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] - 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | 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] - 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo_common.cc:21: + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from misc_streams.h:4, - from misc_streams.cc:5: + from stream.cc:22: stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -3763,56 +4144,42 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | 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] - 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from sequence.cc:21: + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : - | ^~~~~~~~ +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] + 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from sequence.cc:21: + from compress_stream.h:22, + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; - | ^~~~~~~~ + from stream.cc:22: +stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +stream.h: At global scope: +stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -3828,9 +4195,9 @@ 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] - 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : - | ^~~~~~~~ +stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -3842,46 +4209,28 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: +stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from ducttape.h:21, - from ducttape.cc:21: -stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from align.h:20, + from anfo_common.h:22, + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -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] - 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; +stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -3894,22 +4243,23 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +stream.cc:81:30: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 81 | AnfoReader::AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; - | ^~~~~~~~ +stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -3921,53 +4271,28 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from sequence.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | 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] - 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from sequence.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | 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] - 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: +stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -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] - 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; +stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -3980,6 +4305,12 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: +stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -3987,103 +4318,107 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo_common.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | 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] - 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from sequence.cc:21: + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : - | ^~~~~~~~ -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] - 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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] + 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] + 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from ducttape.cc:21: -stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : - | ^~~~~~~~ +In file included from stream.h:20, + from sequence.cc:23: +compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': +compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 198 | else if( r != Z_OK ) throw zs_.msg ; + | ^~~~~~~~~~~~~ +compress_stream.h:198:26: 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] + 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from ducttape.cc:21: -stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ +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] + 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from ducttape.cc:21: -stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; - | ^~~~~~~~ +stream.cc: In member function 'virtual void streams::ChunkedWriter::put_result(const output::Result&)': +stream.cc:344:27: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] + 344 | flush_buffer( r.ByteSize() ) ; + | ^ +In file included from /usr/include/google/protobuf/generated_enum_util.h:36, + from /usr/include/google/protobuf/map.h:49, + from /usr/include/google/protobuf/generated_message_table_driven.h:34, + from output.pb.h:26, + from stream.h:22, + from misc_streams.h:4, + from stream.cc:22: +/usr/include/google/protobuf/message_lite.h:408:7: note: declared here + 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } + | ^~~~~~~~ +stream.cc: At global scope: +stream.cc:421:36: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 421 | ChunkedReader::ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; - | ^~~~~~~~ +In file included from stream.h:20, + from sequence.cc:23: +compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': +compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 379 | else if( r < BZ_OK ) throw BzipError( r ) ; + | ^~~~~~~~~~~~~~~~~~~~ +compress_stream.h:379:26: 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] + 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -4094,7 +4429,7 @@ | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -4105,13 +4440,13 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : | ^~~~~~~~ @@ -4122,64 +4457,48 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from ducttape.cc:21: -stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; - | ^~~~~~~~ +stream.cc:1093:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1093 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ +stream.cc:1114:29: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1114 | StreamWithProgress( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, int64_t total ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : - | ^~~~~~~~ +stream.cc:1149:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1149 | StreamHolder make_input_stream_( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, bool solexa_scores, char origin, const string& genome ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + from anfo-elk.cc:27: +stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -4188,16 +4507,16 @@ 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; - | ^~~~~~~~ + from anfo-elk.cc:27: +stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -4205,64 +4524,48 @@ 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: -stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ +stream.cc: In function 'streams::StreamHolder streams::{anonymous}::make_input_stream_(std::auto_ptr, const string&, bool, char, const string&)': +stream.cc:1179:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1179 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > bs( new BunzipStream( is ) ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from compress_stream.h:22, + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: -stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : - | ^~~~~~~~ +stream.cc:1189:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1189 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > zs( new InflateStream( is ) ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from compress_stream.h:22, + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; - | ^~~~~~~~ +stream.cc: In member function 'virtual output::Header streams::UniversalReader::fetch_header()': +stream.cc:1233:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1233 | std::auto_ptr< google::protobuf::io::FileInputStream > s( new google::protobuf::io::FileInputStream( fd ) ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -4273,13 +4576,24 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +stream.cc:1238:12: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1238 | std::auto_ptr(s), name_, st.st_size ) ) ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : | ^~~~~~~~ @@ -4290,13 +4604,25 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +stream.cc: At global scope: +stream.cc:1378:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1378 | BamReader::BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) : + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -4307,13 +4633,13 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; | ^~~~~~~~ @@ -4324,13 +4650,13 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; | ^~~~~~~~ @@ -4341,576 +4667,432 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +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] 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | 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] - 139 | std::auto_ptr< std::ostream > out_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -stream.cc:81:30: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 81 | AnfoReader::AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name ) - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | 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] - 139 | std::auto_ptr< std::ostream > out_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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 index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from index-test.cc:30: stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from output_streams.cc:21: -output_streams.h:45:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 45 | auto_ptr< std::ostream > out_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from output_streams.cc:21: -output_streams.h:72:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 72 | std::auto_ptr< std::ostream > out_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.cc:21: -output_streams.h:123:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 123 | std::auto_ptr< std::ostream > out_ ; +In file included from anfo-elk.cc:28: +ducttape.h:139:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 139 | std::auto_ptr< std::ostream > out_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + 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++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.cc:21: -output_streams.h:138:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 138 | std::auto_ptr< std::ostream > out_ ; +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] + 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.cc:21: -output_streams.h:149:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 149 | std::auto_ptr< std::ostream > out_ ; - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.cc:21: -output_streams.h:176:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 176 | std::auto_ptr< std::ostream > out_ ; +In file included from sequence.cc:23: +stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -stream.cc: In member function 'virtual void streams::ChunkedWriter::put_result(const output::Result&)': -stream.cc:344:27: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] - 344 | flush_buffer( r.ByteSize() ) ; - | ^ -In file included from /usr/include/google/protobuf/generated_enum_util.h:36, - from /usr/include/google/protobuf/map.h:49, - from /usr/include/google/protobuf/generated_message_table_driven.h:34, - from output.pb.h:26, - from stream.h:22, - from misc_streams.h:4, - from stream.cc:22: -/usr/include/google/protobuf/message_lite.h:408:7: note: declared here - 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } - | ^~~~~~~~ -stream.cc: At global scope: -stream.cc:421:36: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 421 | ChunkedReader::ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name ) - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -stream.cc:1093:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1093 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -stream.cc:1114:29: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1114 | StreamWithProgress( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, int64_t total ) - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -stream.cc:1149:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1149 | StreamHolder make_input_stream_( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, bool solexa_scores, char origin, const string& genome ) - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -stream.cc: In function 'streams::StreamHolder streams::{anonymous}::make_input_stream_(std::auto_ptr, const string&, bool, char, const string&)': -stream.cc:1179:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1179 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > bs( new BunzipStream( is ) ) ; - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -stream.cc:1189:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1189 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > zs( new InflateStream( is ) ) ; - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -stream.cc: In member function 'virtual output::Header streams::UniversalReader::fetch_header()': -stream.cc:1233:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1233 | std::auto_ptr< google::protobuf::io::FileInputStream > s( new google::protobuf::io::FileInputStream( fd ) ) ; - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -stream.cc:1238:12: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1238 | std::auto_ptr(s), name_, st.st_size ) ) ; - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -stream.cc: At global scope: -stream.cc:1378:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1378 | BamReader::BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) : - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-tool.cc:24: -output_streams.h:45:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 45 | auto_ptr< std::ostream > out_ ; - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-tool.cc:24: -output_streams.h:72:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 72 | std::auto_ptr< std::ostream > out_ ; +In file included from sequence.cc:23: +stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-tool.cc:24: -output_streams.h:123:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 123 | std::auto_ptr< std::ostream > out_ ; - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-tool.cc:24: -output_streams.h:138:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 138 | std::auto_ptr< std::ostream > out_ ; +In file included from sequence.cc:23: +stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-tool.cc:24: -output_streams.h:149:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 149 | std::auto_ptr< std::ostream > out_ ; - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-tool.cc:24: -output_streams.h:176:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 176 | std::auto_ptr< std::ostream > out_ ; +In file included from sequence.cc:23: +stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ @@ -5004,20 +5186,6 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 489 | auto_ptr< istream > deffile( p.first ) ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: stream.h: In instantiation of 'void streams::write_delimited_message(google::protobuf::io::CodedOutputStream&, int, const Msg&) [with Msg = output::Header]': @@ -5072,12 +5240,6 @@ /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ -In file included from anfo-tool.cc:23: -misc_streams.h: In instantiation of 'void streams::SortingStream::put_result(const output::Result&) [with Comp = streams::by_seqid]': -misc_streams.h:282:16: required from here -misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] - 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from anfo-elk.cc:30: misc_streams.h: In instantiation of 'void streams::SortingStream::put_result(const output::Result&) [with Comp = streams::by_seqid]': misc_streams.h:282:16: required from here @@ -5087,24 +5249,12 @@ In file included from output.pb.h:31, from sequence.h:32, from align_fwd.h:5, - from ducttape.h:20, - from anfo-tool.cc:22: -/usr/include/google/protobuf/message.h:299:7: note: declared here - 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } - | ^~~~~~~~~ -In file included from output.pb.h:31, - from sequence.h:32, - from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/google/protobuf/message.h:299:7: note: declared here 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } | ^~~~~~~~~ -In file included from anfo-tool.cc:23: -misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] - 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from anfo-elk.cc:30: misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; @@ -5112,46 +5262,12 @@ In file included from output.pb.h:31, from sequence.h:32, from align_fwd.h:5, - from ducttape.h:20, - from anfo-tool.cc:22: -/usr/include/google/protobuf/message.h:299:7: note: declared here - 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } - | ^~~~~~~~~ -In file included from output.pb.h:31, - from sequence.h:32, - from align_fwd.h:5, from align.h:20, from anfo_common.h:22, from anfo-elk.cc:27: /usr/include/google/protobuf/message.h:299:7: note: declared here 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } | ^~~~~~~~~ -In file included from anfo-tool.cc:23: -misc_streams.h: In instantiation of 'void streams::SortingStream::put_result(const output::Result&) [with Comp = streams::by_genome_coordinate]': -misc_streams.h:282:16: required from here -misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] - 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -In file included from output.pb.h:31, - from sequence.h:32, - from align_fwd.h:5, - from ducttape.h:20, - from anfo-tool.cc:22: -/usr/include/google/protobuf/message.h:299:7: note: declared here - 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } - | ^~~~~~~~~ -In file included from anfo-tool.cc:23: -misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] - 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -In file included from output.pb.h:31, - from sequence.h:32, - from align_fwd.h:5, - from ducttape.h:20, - from anfo-tool.cc:22: -/usr/include/google/protobuf/message.h:299:7: note: declared here - 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } - | ^~~~~~~~~ In file included from anfo-elk.cc:30: misc_streams.h: In instantiation of 'void streams::SortingStream::put_result(const output::Result&) [with Comp = streams::by_genome_coordinate]': misc_streams.h:282:16: required from here @@ -5180,6 +5296,8 @@ /usr/include/google/protobuf/message.h:299:7: note: declared here 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } | ^~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c align.cc -o align.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 stream.h:20, from file-info.cc:25: compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] @@ -5264,101 +5382,6 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from align.cc:21: -compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from align.cc:21: -compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from align.cc:21: -compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': -compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 198 | else if( r != Z_OK ) throw zs_.msg ; - | ^~~~~~~~~~~~~ -compress_stream.h:198:26: 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] - 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from align.cc:21: -compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from align.cc:21: -compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': -compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 379 | else if( r < BZ_OK ) throw BzipError( r ) ; - | ^~~~~~~~~~~~~~~~~~~~ -compress_stream.h:379:26: 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] - 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ In file included from file-info.cc:25: stream.h: At global scope: stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] @@ -5464,61 +5487,70 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from file-info.cc:25: -stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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] + 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from file-info.cc:21: + from compress_stream.h:22, + from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from file-info.cc:25: -stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : - | ^~~~~~~~ +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] + 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from file-info.cc:21: + from compress_stream.h:22, + from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from file-info.cc:25: -stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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] + 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from file-info.cc:21: + from compress_stream.h:22, + from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from file-info.cc:25: -stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : - | ^~~~~~~~ +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] + 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from file-info.cc:21: + from compress_stream.h:22, + from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from file-info.cc:25: -stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -5530,9 +5562,9 @@ 57 | template class auto_ptr; | ^~~~~~~~ In file included from file-info.cc:25: -stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : - | ^~~~~~~~ +stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -5542,23 +5574,30 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from file-info.cc:25: -stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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] + 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from file-info.cc:21: + from compress_stream.h:22, + from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] + 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from file-info.cc:25: -stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; - | ^~~~~~~~ +stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -5569,9 +5608,9 @@ 57 | template class auto_ptr; | ^~~~~~~~ In file included from file-info.cc:25: -stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; - | ^~~~~~~~ +stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -5581,293 +5620,289 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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] - 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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 misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 323 | 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:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer + | ^~~~~~~~ +In file included from file-info.cc:25: +stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from align.cc:21: + from file-info.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | 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] - 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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 misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from align.cc:21: -stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output - | ^~~~~~~~ +In file included from file-info.cc:25: +stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from align.cc:21: + from file-info.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from align.cc:21: -stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 387 | 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:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ +In file included from file-info.cc:25: +stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from align.cc:21: + from file-info.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from align.cc:21: -stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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 misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from align.cc:21: -stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer - | ^~~~~~~~ +In file included from file-info.cc:25: +stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from align.cc:21: + from file-info.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from align.cc:21: -stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +In file included from file-info.cc:25: +stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from align.cc:21: + from file-info.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from align.cc:21: +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] 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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 misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from align.cc:21: +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] 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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 misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from align.cc:21: +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] 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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 misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from align.cc:21: +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] 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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 misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from align.cc:21: +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] 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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 misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from align.cc:21: +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] 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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 misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from align.cc:21: +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] 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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 misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from align.cc:21: +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] 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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 misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from align.cc:21: +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] 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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 misc_streams.h:4, + from misc_streams.cc:5: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | 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] + 489 | auto_ptr< istream > deffile( p.first ) ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c align.cc -o align.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c config.pb.cc -o config.pb.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c output_streams.cc -o output_streams.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c config.pb.cc -o config.pb.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c index.cc -o index.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/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 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo-elk.cc -o anfo-elk.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -lpthread -lelk -lbz2 -lz -lpopt +/bin/sh ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -lpthread -lelk -lbz2 -lz -lpopt libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/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/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../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/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -pthread -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libanfo.so.0 -o .libs/libanfo.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libanfo.so.0" && ln -s "libanfo.so.0.0.0" "libanfo.so.0") libtool: link: (cd ".libs" && rm -f "libanfo.so" && ln -s "libanfo.so.0.0.0" "libanfo.so") libtool: link: ar cr .libs/libanfo.a align.o anfo_common.o concurrent_stream.o ducttape.o index.o misc_streams.o output_streams.o sequence.o stream.o util.o anfo-elk.o fastlz.o config.pb.o output.pb.o libtool: link: ranlib .libs/libanfo.a libtool: link: ( cd ".libs" && rm -f "libanfo.la" && ln -s "../libanfo.la" "libanfo.la" ) -/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fa2dna fa2dna.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt -/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o dnaindex dnaindex.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt -/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -lelk -lbz2 -lz -lpopt -/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o anfo anfo.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt -/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -lelk -lbz2 -lz -lpopt -/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -lelk -lbz2 -lz -lpopt +/bin/sh ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fa2dna fa2dna.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt +/bin/sh ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o dnaindex dnaindex.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt +/bin/sh ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -lelk -lbz2 -lz -lpopt +/bin/sh ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o anfo anfo.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt +/bin/sh ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -lelk -lbz2 -lz -lpopt +/bin/sh ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -lelk -lbz2 -lz -lpopt +libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread +libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/fa2dna fa2dna.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread -libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/dnaindex dnaindex.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread -libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread -libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/anfo anfo.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread +libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/dnaindex dnaindex.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread make[4]: Leaving directory '/build/reproducible-path/anfo-0.98/src' make[3]: Leaving directory '/build/reproducible-path/anfo-0.98/src' Making all in man @@ -5879,7 +5914,7 @@ make[2]: Leaving directory '/build/reproducible-path/anfo-0.98' make[1]: Leaving directory '/build/reproducible-path/anfo-0.98' dh_auto_test - make -j42 check VERBOSE=1 + make -j20 check VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/anfo-0.98' Making check in src make[2]: Entering directory '/build/reproducible-path/anfo-0.98/src' @@ -5895,7 +5930,7 @@ make[2]: Entering directory '/build/reproducible-path/anfo-0.98' make[2]: Leaving directory '/build/reproducible-path/anfo-0.98' make[1]: Leaving directory '/build/reproducible-path/anfo-0.98' - rm -fr -- /tmp/dh-xdg-rundir-cvmYvUmQ + rm -fr -- /tmp/dh-xdg-rundir-hGxx6RA9 create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/anfo.substvars debian/libanfo0.substvars debian/libanfo0-dev.substvars @@ -5910,7 +5945,7 @@ make[3]: Entering directory '/build/reproducible-path/anfo-0.98/src' make[4]: Entering directory '/build/reproducible-path/anfo-0.98/src' /bin/mkdir -p '/build/reproducible-path/anfo-0.98/debian/tmp/usr/lib/x86_64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libanfo.la '/build/reproducible-path/anfo-0.98/debian/tmp/usr/lib/x86_64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libanfo.la '/build/reproducible-path/anfo-0.98/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libanfo.so.0.0.0 /build/reproducible-path/anfo-0.98/debian/tmp/usr/lib/x86_64-linux-gnu/libanfo.so.0.0.0 libtool: install: (cd /build/reproducible-path/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/reproducible-path/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; }; }) @@ -5920,7 +5955,7 @@ libtool: install: ranlib /build/reproducible-path/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/reproducible-path/anfo-0.98/debian/tmp/usr/bin' - /bin/bash ../libtool --mode=install /usr/bin/install -c fa2dna dnaindex anfo-tool anfo '/build/reproducible-path/anfo-0.98/debian/tmp/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c fa2dna dnaindex anfo-tool anfo '/build/reproducible-path/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/reproducible-path/anfo-0.98/debian/tmp/usr/bin/fa2dna libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/x86_64-linux-gnu' @@ -5930,7 +5965,7 @@ libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/anfo /build/reproducible-path/anfo-0.98/debian/tmp/usr/bin/anfo /bin/mkdir -p '/build/reproducible-path/anfo-0.98/debian/tmp/usr/libexec' - /bin/bash ../libtool --mode=install /usr/bin/install -c index-test file-info '/build/reproducible-path/anfo-0.98/debian/tmp/usr/libexec' + /bin/sh ../libtool --mode=install /usr/bin/install -c index-test file-info '/build/reproducible-path/anfo-0.98/debian/tmp/usr/libexec' 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/reproducible-path/anfo-0.98/debian/tmp/usr/libexec/index-test libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/x86_64-linux-gnu' @@ -6005,9 +6040,9 @@ install -d debian/libanfo0-dev/usr/share/doc/libanfo0-dev install -p -m0644 debian/copyright debian/libanfo0-dev/usr/share/doc/libanfo0-dev/copyright dh_installchangelogs - install -p -m0644 debian/changelog debian/libanfo0-dev/usr/share/doc/libanfo0-dev/changelog.Debian install -p -m0644 debian/changelog debian/anfo/usr/share/doc/anfo/changelog.Debian install -p -m0644 debian/changelog debian/libanfo0/usr/share/doc/libanfo0/changelog.Debian + install -p -m0644 debian/changelog debian/libanfo0-dev/usr/share/doc/libanfo0-dev/changelog.Debian rm -f debian/anfo.debhelper.log debian/libanfo0-dev.debhelper.log debian/libanfo0.debhelper.log debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/anfo-0.98' @@ -6017,20 +6052,20 @@ man-recode --to-code UTF-8 --suffix .dh-new debian/anfo/usr/share/man/man1/anfo-tool.1 man-recode --to-code UTF-8 --suffix .dh-new debian/anfo/usr/share/man/man1/anfo.1 man-recode --to-code UTF-8 --suffix .dh-new debian/anfo/usr/share/man/man1/dnaindex.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/anfo/usr/share/man/man1/fa2dna.1 man-recode --to-code UTF-8 --suffix .dh-new debian/anfo/usr/share/man/man1/file-info.1 - mv debian/anfo/usr/share/man/man1/anfo.1.dh-new debian/anfo/usr/share/man/man1/anfo.1 - chmod 0644 -- debian/anfo/usr/share/man/man1/anfo.1 - mv debian/anfo/usr/share/man/man1/anfo-sge.1.dh-new debian/anfo/usr/share/man/man1/anfo-sge.1 - chmod 0644 -- debian/anfo/usr/share/man/man1/anfo-sge.1 - mv debian/anfo/usr/share/man/man1/anfo-tool.1.dh-new debian/anfo/usr/share/man/man1/anfo-tool.1 - chmod 0644 -- debian/anfo/usr/share/man/man1/anfo-tool.1 - mv debian/anfo/usr/share/man/man1/dnaindex.1.dh-new debian/anfo/usr/share/man/man1/dnaindex.1 - chmod 0644 -- debian/anfo/usr/share/man/man1/dnaindex.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/anfo/usr/share/man/man1/fa2dna.1 mv debian/anfo/usr/share/man/man1/file-info.1.dh-new debian/anfo/usr/share/man/man1/file-info.1 chmod 0644 -- debian/anfo/usr/share/man/man1/file-info.1 + mv debian/anfo/usr/share/man/man1/anfo-tool.1.dh-new debian/anfo/usr/share/man/man1/anfo-tool.1 + chmod 0644 -- debian/anfo/usr/share/man/man1/anfo-tool.1 mv debian/anfo/usr/share/man/man1/fa2dna.1.dh-new debian/anfo/usr/share/man/man1/fa2dna.1 chmod 0644 -- debian/anfo/usr/share/man/man1/fa2dna.1 + mv debian/anfo/usr/share/man/man1/anfo-sge.1.dh-new debian/anfo/usr/share/man/man1/anfo-sge.1 + chmod 0644 -- debian/anfo/usr/share/man/man1/anfo-sge.1 + mv debian/anfo/usr/share/man/man1/anfo.1.dh-new debian/anfo/usr/share/man/man1/anfo.1 + chmod 0644 -- debian/anfo/usr/share/man/man1/anfo.1 + mv debian/anfo/usr/share/man/man1/dnaindex.1.dh-new debian/anfo/usr/share/man/man1/dnaindex.1 + chmod 0644 -- debian/anfo/usr/share/man/man1/dnaindex.1 # delete unused manpage find debian/anfo -name anfo-sge.1 -delete make[1]: Leaving directory '/build/reproducible-path/anfo-0.98' @@ -6043,38 +6078,38 @@ dh_strip_nondeterminism dh_compress cd debian/anfo - cd debian/libanfo0 cd debian/libanfo0-dev + cd debian/libanfo0 chmod a-x usr/share/doc/anfo/README usr/share/doc/anfo/changelog.Debian usr/share/man/man1/anfo-tool.1 usr/share/man/man1/anfo.1 usr/share/man/man1/dnaindex.1 usr/share/man/man1/fa2dna.1 usr/share/man/man1/file-info.1 chmod a-x usr/share/doc/libanfo0/changelog.Debian - chmod a-x usr/share/doc/libanfo0-dev/changelog.Debian gzip -9nf usr/share/doc/anfo/README usr/share/doc/anfo/changelog.Debian usr/share/man/man1/anfo-tool.1 usr/share/man/man1/anfo.1 usr/share/man/man1/dnaindex.1 usr/share/man/man1/fa2dna.1 usr/share/man/man1/file-info.1 gzip -9nf usr/share/doc/libanfo0/changelog.Debian - gzip -9nf usr/share/doc/libanfo0-dev/changelog.Debian + chmod a-x usr/share/doc/libanfo0-dev/changelog.Debian cd '/build/reproducible-path/anfo-0.98' + gzip -9nf usr/share/doc/libanfo0-dev/changelog.Debian cd '/build/reproducible-path/anfo-0.98' cd '/build/reproducible-path/anfo-0.98' rm -f debian/anfo.debhelper.log debian/libanfo0-dev.debhelper.log debian/libanfo0.debhelper.log debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/anfo-0.98' dh_fixperms + find debian/libanfo0-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/anfo ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libanfo0 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s - find debian/libanfo0-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s - find debian/libanfo0/usr/share/doc -type f -a -true -a ! -regex 'debian/libanfo0/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libanfo0-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libanfo0-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/anfo/usr/share/doc -type f -a -true -a ! -regex 'debian/anfo/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libanfo0/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/libanfo0/usr/share/doc -type f -a -true -a ! -regex 'debian/libanfo0/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libanfo0-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/anfo/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/anfo/usr/share/doc -type f -a -true -a ! -regex 'debian/anfo/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libanfo0-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/anfo/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/libanfo0/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/libanfo0-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/anfo/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libanfo0 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/anfo -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libanfo0-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libanfo0/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w - find debian/anfo/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/libanfo0-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w + find debian/anfo/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x + find debian/libanfo0/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/anfo/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/anfo -perm -5 -type f \( -name '*.scm' \) -print0 2>/dev/null | xargs -0r chmod 644 make[1]: Leaving directory '/build/reproducible-path/anfo-0.98' @@ -6086,28 +6121,8 @@ dwz -- debian/libanfo0/usr/lib/x86_64-linux-gnu/libanfo.so.0.0.0 dh_strip -a strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/libanfo0-dev/usr/lib/x86_64-linux-gnu/libanfo.a - install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b7 - objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/bin/dnaindex debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b7/5552da628ddbb623cd392388fd4d0cdcd6214b.debug install -d debian/.debhelper/libanfo0/dbgsym-root/usr/lib/debug/.build-id/51 objcopy --only-keep-debug --compress-debug-sections debian/libanfo0/usr/lib/x86_64-linux-gnu/libanfo.so.0.0.0 debian/.debhelper/libanfo0/dbgsym-root/usr/lib/debug/.build-id/51/e1bc507796b73daab9de0c26517136f4464d95.debug - chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b7/5552da628ddbb623cd392388fd4d0cdcd6214b.debug - strip --remove-section=.comment --remove-section=.note debian/anfo/usr/bin/dnaindex - objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b7/5552da628ddbb623cd392388fd4d0cdcd6214b.debug debian/anfo/usr/bin/dnaindex - install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/34 - objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/bin/anfo debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/34/57f02b19e2b0d0cc22c763f32f09257bf7df78.debug - chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/34/57f02b19e2b0d0cc22c763f32f09257bf7df78.debug - strip --remove-section=.comment --remove-section=.note debian/anfo/usr/bin/anfo - objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/34/57f02b19e2b0d0cc22c763f32f09257bf7df78.debug debian/anfo/usr/bin/anfo - install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/90 - objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/bin/fa2dna debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/90/5d6a6a81b0a1628c2b68f5d9aca470718194ca.debug - chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/90/5d6a6a81b0a1628c2b68f5d9aca470718194ca.debug - strip --remove-section=.comment --remove-section=.note debian/anfo/usr/bin/fa2dna - objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/90/5d6a6a81b0a1628c2b68f5d9aca470718194ca.debug debian/anfo/usr/bin/fa2dna - install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b0 - objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/bin/anfo-tool debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b0/795aa4cebf2674892c31eec060865e8ebc8f06.debug - chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b0/795aa4cebf2674892c31eec060865e8ebc8f06.debug - strip --remove-section=.comment --remove-section=.note debian/anfo/usr/bin/anfo-tool - objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b0/795aa4cebf2674892c31eec060865e8ebc8f06.debug debian/anfo/usr/bin/anfo-tool install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/4f objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/lib/anfo/file-info debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/4f/8c39205a7c0ec03785b22d537b3ea3fc9225bb.debug chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/4f/8c39205a7c0ec03785b22d537b3ea3fc9225bb.debug @@ -6118,17 +6133,37 @@ chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/1d/b275ae9b899172141237c1ccaba01f9e473001.debug strip --remove-section=.comment --remove-section=.note debian/anfo/usr/lib/anfo/index-test objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/1d/b275ae9b899172141237c1ccaba01f9e473001.debug debian/anfo/usr/lib/anfo/index-test + install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/90 + objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/bin/fa2dna debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/90/5d6a6a81b0a1628c2b68f5d9aca470718194ca.debug + chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/90/5d6a6a81b0a1628c2b68f5d9aca470718194ca.debug + strip --remove-section=.comment --remove-section=.note debian/anfo/usr/bin/fa2dna + objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/90/5d6a6a81b0a1628c2b68f5d9aca470718194ca.debug debian/anfo/usr/bin/fa2dna + chmod 0644 -- debian/.debhelper/libanfo0/dbgsym-root/usr/lib/debug/.build-id/51/e1bc507796b73daab9de0c26517136f4464d95.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libanfo0/usr/lib/x86_64-linux-gnu/libanfo.so.0.0.0 + objcopy --add-gnu-debuglink debian/.debhelper/libanfo0/dbgsym-root/usr/lib/debug/.build-id/51/e1bc507796b73daab9de0c26517136f4464d95.debug debian/libanfo0/usr/lib/x86_64-linux-gnu/libanfo.so.0.0.0 + install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/34 + objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/bin/anfo debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/34/57f02b19e2b0d0cc22c763f32f09257bf7df78.debug + chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/34/57f02b19e2b0d0cc22c763f32f09257bf7df78.debug + strip --remove-section=.comment --remove-section=.note debian/anfo/usr/bin/anfo + install -d debian/.debhelper/libanfo0/dbgsym-root/usr/share/doc + ln -s libanfo0 debian/.debhelper/libanfo0/dbgsym-root/usr/share/doc/libanfo0-dbgsym + objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/34/57f02b19e2b0d0cc22c763f32f09257bf7df78.debug debian/anfo/usr/bin/anfo + install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b7 + objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/bin/dnaindex debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b7/5552da628ddbb623cd392388fd4d0cdcd6214b.debug + chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b7/5552da628ddbb623cd392388fd4d0cdcd6214b.debug + strip --remove-section=.comment --remove-section=.note debian/anfo/usr/bin/dnaindex + objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b7/5552da628ddbb623cd392388fd4d0cdcd6214b.debug debian/anfo/usr/bin/dnaindex + install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b0 + objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/bin/anfo-tool debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b0/795aa4cebf2674892c31eec060865e8ebc8f06.debug + chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b0/795aa4cebf2674892c31eec060865e8ebc8f06.debug + strip --remove-section=.comment --remove-section=.note debian/anfo/usr/bin/anfo-tool + objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/b0/795aa4cebf2674892c31eec060865e8ebc8f06.debug debian/anfo/usr/bin/anfo-tool install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/anfo/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/anfo/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/anfo/usr/lib/debug install -d debian/.debhelper/anfo/dbgsym-root/usr/share/doc ln -s anfo debian/.debhelper/anfo/dbgsym-root/usr/share/doc/anfo-dbgsym - chmod 0644 -- debian/.debhelper/libanfo0/dbgsym-root/usr/lib/debug/.build-id/51/e1bc507796b73daab9de0c26517136f4464d95.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libanfo0/usr/lib/x86_64-linux-gnu/libanfo.so.0.0.0 - objcopy --add-gnu-debuglink debian/.debhelper/libanfo0/dbgsym-root/usr/lib/debug/.build-id/51/e1bc507796b73daab9de0c26517136f4464d95.debug debian/libanfo0/usr/lib/x86_64-linux-gnu/libanfo.so.0.0.0 - install -d debian/.debhelper/libanfo0/dbgsym-root/usr/share/doc - ln -s libanfo0 debian/.debhelper/libanfo0/dbgsym-root/usr/share/doc/libanfo0-dbgsym dh_makeshlibs -a rm -f debian/anfo/DEBIAN/shlibs rm -f debian/libanfo0/DEBIAN/shlibs @@ -6140,7 +6175,7 @@ dh_shlibdeps -a dpkg-shlibdeps -Tdebian/libanfo0.substvars debian/libanfo0/usr/lib/x86_64-linux-gnu/libanfo.so.0.0.0 install -d debian/anfo/DEBIAN - dpkg-shlibdeps -Tdebian/anfo.substvars debian/anfo/usr/bin/dnaindex debian/anfo/usr/bin/anfo debian/anfo/usr/bin/fa2dna debian/anfo/usr/bin/anfo-tool debian/anfo/usr/lib/anfo/file-info debian/anfo/usr/lib/anfo/index-test + dpkg-shlibdeps -Tdebian/anfo.substvars debian/anfo/usr/lib/anfo/file-info debian/anfo/usr/lib/anfo/index-test debian/anfo/usr/bin/fa2dna debian/anfo/usr/bin/anfo debian/anfo/usr/bin/dnaindex debian/anfo/usr/bin/anfo-tool dh_installdeb install -p -m0644 debian/.debhelper/generated/libanfo0/triggers debian/libanfo0/DEBIAN/triggers install -d debian/libanfo0-dev/DEBIAN @@ -6148,19 +6183,19 @@ echo misc:Depends= >> debian/libanfo0-dev.substvars echo misc:Pre-Depends= >> debian/libanfo0-dev.substvars dpkg-gencontrol -plibanfo0-dev -ldebian/changelog -Tdebian/libanfo0-dev.substvars -Pdebian/libanfo0-dev - echo misc:Depends= >> debian/libanfo0.substvars - echo misc:Pre-Depends= >> debian/libanfo0.substvars - install -d debian/.debhelper/libanfo0/dbgsym-root/DEBIAN - dpkg-gencontrol -plibanfo0 -ldebian/changelog -Tdebian/libanfo0.substvars -Pdebian/.debhelper/libanfo0/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=libanfo0-dbgsym "-DDepends=libanfo0 (= \${binary:Version})" "-DDescription=debug symbols for libanfo0" -DBuild-Ids=51e1bc507796b73daab9de0c26517136f4464d95 -DSection=debug -UMulti-Arch -UReplaces -UBreaks echo misc:Depends= >> debian/anfo.substvars echo misc:Pre-Depends= >> debian/anfo.substvars install -d debian/.debhelper/anfo/dbgsym-root/DEBIAN dpkg-gencontrol -panfo -ldebian/changelog -Tdebian/anfo.substvars -Pdebian/.debhelper/anfo/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=anfo-dbgsym "-DDepends=anfo (= \${binary:Version})" "-DDescription=debug symbols for anfo" "-DBuild-Ids=1db275ae9b899172141237c1ccaba01f9e473001 3457f02b19e2b0d0cc22c763f32f09257bf7df78 4f8c39205a7c0ec03785b22d537b3ea3fc9225bb 905d6a6a81b0a1628c2b68f5d9aca470718194ca b0795aa4cebf2674892c31eec060865e8ebc8f06 b75552da628ddbb623cd392388fd4d0cdcd6214b" -DSection=debug -UMulti-Arch -UReplaces -UBreaks + echo misc:Depends= >> debian/libanfo0.substvars + echo misc:Pre-Depends= >> debian/libanfo0.substvars + install -d debian/.debhelper/libanfo0/dbgsym-root/DEBIAN + dpkg-gencontrol -plibanfo0 -ldebian/changelog -Tdebian/libanfo0.substvars -Pdebian/.debhelper/libanfo0/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=libanfo0-dbgsym "-DDepends=libanfo0 (= \${binary:Version})" "-DDescription=debug symbols for libanfo0" -DBuild-Ids=51e1bc507796b73daab9de0c26517136f4464d95 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/libanfo0-dev/DEBIAN/control - chmod 0644 -- debian/.debhelper/libanfo0/dbgsym-root/DEBIAN/control - dpkg-gencontrol -plibanfo0 -ldebian/changelog -Tdebian/libanfo0.substvars -Pdebian/libanfo0 chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/DEBIAN/control dpkg-gencontrol -panfo -ldebian/changelog -Tdebian/anfo.substvars -Pdebian/anfo + chmod 0644 -- debian/.debhelper/libanfo0/dbgsym-root/DEBIAN/control + dpkg-gencontrol -plibanfo0 -ldebian/changelog -Tdebian/libanfo0.substvars -Pdebian/libanfo0 chmod 0644 -- debian/libanfo0/DEBIAN/control chmod 0644 -- debian/anfo/DEBIAN/control dh_md5sums @@ -6168,23 +6203,23 @@ cd debian/anfo >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libanfo0-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/anfo/DEBIAN/md5sums + chmod 0644 -- debian/libanfo0-dev/DEBIAN/md5sums chmod 0644 -- debian/libanfo0/DEBIAN/md5sums cd debian/.debhelper/anfo/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/libanfo0/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - chmod 0644 -- debian/libanfo0-dev/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libanfo0/dbgsym-root/DEBIAN/md5sums dh_builddeb - dpkg-deb --root-owner-group --build debian/anfo .. - dpkg-deb --root-owner-group --build debian/.debhelper/anfo/dbgsym-root .. dpkg-deb --root-owner-group --build debian/libanfo0 .. - dpkg-deb --root-owner-group --build debian/.debhelper/libanfo0/dbgsym-root .. dpkg-deb --root-owner-group --build debian/libanfo0-dev .. + dpkg-deb --root-owner-group --build debian/.debhelper/anfo/dbgsym-root .. + dpkg-deb --root-owner-group --build debian/anfo .. + dpkg-deb --root-owner-group --build debian/.debhelper/libanfo0/dbgsym-root .. +dpkg-deb: building package 'libanfo0-dev' in '../libanfo0-dev_0.98-8_amd64.deb'. dpkg-deb: building package 'anfo' in '../anfo_0.98-8_amd64.deb'. +dpkg-deb: building package 'libanfo0-dbgsym' in '../libanfo0-dbgsym_0.98-8_amd64.deb'. dpkg-deb: building package 'anfo-dbgsym' in '../anfo-dbgsym_0.98-8_amd64.deb'. dpkg-deb: building package 'libanfo0' in '../libanfo0_0.98-8_amd64.deb'. -dpkg-deb: building package 'libanfo0-dbgsym' in '../libanfo0-dbgsym_0.98-8_amd64.deb'. -dpkg-deb: building package 'libanfo0-dev' in '../libanfo0-dev_0.98-8_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../anfo_0.98-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -6192,12 +6227,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1543234/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1543234/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/4031259 and its subdirectories -I: Current time: Sun Aug 31 12:26:14 -12 2025 -I: pbuilder-time-stamp: 1756686374 +I: removing directory /srv/workspace/pbuilder/1543234 and its subdirectories +I: Current time: Tue Jul 30 08:07:38 +14 2024 +I: pbuilder-time-stamp: 1722276458