Diff of the two buildlogs: -- --- b1/build.log 2021-07-07 18:45:08.481060345 +0000 +++ b2/build.log 2021-07-07 18:51:23.747051466 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jul 7 06:42:33 -12 2021 -I: pbuilder-time-stamp: 1625683353 +I: Current time: Wed Aug 10 15:08:11 +14 2022 +I: pbuilder-time-stamp: 1660093691 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ 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.9VcFMA4z/trustedkeys.kbx': General error -gpgv: Signature made Wed Nov 25 07:08:08 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.Oi5BsPKz/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 @@ -33,135 +33,169 @@ 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/14081/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/27766/tmp/hooks/D01_modify_environment starting +debug: Running on codethink11-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/27766/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/27766/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='14081' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=27766 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.VHgMVuVwa9/pbuilderrc_KNhl --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.VHgMVuVwa9/b1 --logfile b1/build.log anfo_0.98-8.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.VHgMVuVwa9/pbuilderrc_YVvY --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.VHgMVuVwa9/b2 --logfile b2/build.log --extrapackages usrmerge anfo_0.98-8.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink10-arm64 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Jun 21 14:26 bash - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 34808 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 34808 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 14264 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 39832 Sep 22 2020 cat - -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown - -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp - -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash - -rwxr-xr-x 1 root root 101384 Sep 22 2020 date - -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd - -rwxr-xr-x 1 root root 89824 Sep 22 2020 df - -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir - -rwxr-xr-x 1 root root 76152 Feb 7 02:38 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 35632 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 64856 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 93744 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln - -rwxr-xr-x 1 root root 52720 Feb 7 2020 login - -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls - -rwxr-xr-x 1 root root 161960 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 51368 Feb 7 02:38 more - -rwsr-xr-x 1 root root 51360 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 14496 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash - -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm - -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 6 21:24 sh -> dash - -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty - -rwsr-xr-x 1 root root 67776 Feb 7 02:38 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 535768 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch - -rwxr-xr-x 1 root root 31512 Sep 22 2020 true - -rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/14081/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Jun 22 2021 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 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 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 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 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 Feb 8 2021 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 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 64856 Feb 8 2021 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 93744 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 161960 Feb 8 2021 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Feb 8 2021 more + -rwsr-xr-x 1 root root 51360 Feb 8 2021 mount + -rwxr-xr-x 1 root root 14496 Feb 8 2021 mountpoint + -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 2021 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 10 15:08 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 9 05:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Feb 8 2021 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Feb 8 2021 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 Feb 8 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/27766/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -289,7 +323,7 @@ Get: 72 http://deb.debian.org/debian bullseye/main arm64 libprotoc23 arm64 3.12.4-1 [703 kB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 pkg-config arm64 0.29.2-1 [63.6 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 protobuf-compiler arm64 3.12.4-1 [74.9 kB] -Fetched 27.5 MB in 1s (38.9 MB/s) +Fetched 27.5 MB in 1s (44.9 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 ... 19646 files and directories currently installed.) @@ -603,8 +637,45 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (1937 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 23001 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/anfo-0.98/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../anfo_0.98-8_source.changes +hostname: Temporary failure in name resolution +I: Running cd /build/anfo-0.98/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && 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 @@ -692,7 +763,7 @@ ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a thread-safe mkdir -p... /bin/mkdir -p +checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -712,10 +783,10 @@ checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none -checking for a sed that does not truncate output... /bin/sed -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E -checking for fgrep... /bin/grep -F +checking for a sed that does not truncate output... /usr/bin/sed +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E +checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B @@ -735,8 +806,8 @@ checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no -checking for a working dd... /bin/dd -checking how to truncate binary pipes... /bin/dd bs=4096 count=1 +checking for a working dd... /usr/bin/dd +checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E @@ -857,20 +928,20 @@ make all-am make[4]: Entering directory '/build/anfo-0.98/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fa2dna.o fa2dna.cc -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o align.lo align.cc -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo_common.lo anfo_common.cc -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o concurrent_stream.lo concurrent_stream.cc -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ducttape.lo ducttape.cc -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o index.lo index.cc -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o misc_streams.lo misc_streams.cc -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o output_streams.lo output_streams.cc -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c align.cc -fPIC -DPIC -o .libs/align.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c index.cc -fPIC -DPIC -o .libs/index.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_streams.cc -fPIC -DPIC -o .libs/misc_streams.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o align.lo align.cc +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo_common.lo anfo_common.cc +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o concurrent_stream.lo concurrent_stream.cc +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ducttape.lo ducttape.cc +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o index.lo index.cc +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o misc_streams.lo misc_streams.cc +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o output_streams.lo output_streams.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c concurrent_stream.cc -fPIC -DPIC -o .libs/concurrent_stream.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_streams.cc -fPIC -DPIC -o .libs/misc_streams.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c ducttape.cc -fPIC -DPIC -o .libs/ducttape.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo_common.cc -fPIC -DPIC -o .libs/anfo_common.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c index.cc -fPIC -DPIC -o .libs/index.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c align.cc -fPIC -DPIC -o .libs/align.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c output_streams.cc -fPIC -DPIC -o .libs/output_streams.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c ducttape.cc -fPIC -DPIC -o .libs/ducttape.o In file included from stream.h:20, from concurrent_stream.h:23, from concurrent_stream.cc:1: @@ -984,69 +1055,12 @@ 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 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 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 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 /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 /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, @@ -1059,22 +1073,6 @@ 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/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: @@ -1102,28 +1100,6 @@ | ^~~~~~~~~~~~~ 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: 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: @@ -1305,94 +1281,239 @@ /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: 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 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 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: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 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: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 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: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.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: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.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: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 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: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 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: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.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: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: +/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 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 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 ) ; - | ^~~~~~~~ +In file included from stream.h:20, + from ducttape.h:21, + from ducttape.cc:21: +compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 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_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 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 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, + 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_ ; | ^~~~~~~~ In 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 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 stream.h:20, + from ducttape.h:21, + from ducttape.cc:21: +compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 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_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 align.h:22, - from anfo_common.h:22, - from anfo_common.cc:21: -stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer - | ^~~~~~~~ +In file included from stream.h:20, + from ducttape.h:21, + from ducttape.cc:21: +compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': +compress_stream.h:379:26: 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_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 concurrent_stream.h:23, - from concurrent_stream.cc:1: +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_ ; @@ -1400,19 +1521,20 @@ In 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_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: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, @@ -1427,8 +1549,8 @@ 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: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, @@ -1443,9 +1565,10 @@ | ^~~~~~~~ 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 ) ; - | ^~~~~~~~ +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, @@ -1456,20 +1579,18 @@ /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 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 /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.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; | ^~~~~~~~ @@ -1503,64 +1624,20 @@ /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: 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: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: -/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/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: +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/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_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ @@ -1624,98 +1701,106 @@ /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 align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 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 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: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 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: -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_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 /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 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 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/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_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 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 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_ ; | ^~~~~~~~ In 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 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 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 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 ) : + | ^~~~~~~~ In 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 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 misc_streams.cc:5: +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_ ; | ^~~~~~~~ @@ -1724,13 +1809,13 @@ 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 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 misc_streams.cc:5: +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 ) : | ^~~~~~~~ @@ -1739,13 +1824,13 @@ 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 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 misc_streams.cc:5: +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_ ; | ^~~~~~~~ @@ -1754,102 +1839,130 @@ 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 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 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 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 ) : + | ^~~~~~~~ In 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.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 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 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_ ; + | ^~~~~~~~ In 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 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 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 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 ) ; + | ^~~~~~~~ In 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.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 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 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_ ; | ^~~~~~~~ In 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 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 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 ) ; - | ^~~~~~~~ +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 misc_streams.h:4, - from misc_streams.cc:5: + 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 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 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: +/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 misc_streams.h:4, - from misc_streams.cc:5: + 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; | ^~~~~~~~ @@ -1955,36 +2068,6 @@ /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: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: -/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: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: -/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: @@ -2002,10 +2085,11 @@ /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, +In file included from stream.h:20, + 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_ ; +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, @@ -2017,11 +2101,12 @@ /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, +In file included from stream.h:20, + 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 ) : - | ^~~~~~~~ +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, @@ -2032,325 +2117,350 @@ /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_ ; +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 /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 /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 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 ) : - | ^~~~~~~~ +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 concurrent_stream.h:23, - from concurrent_stream.cc:1: + 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 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_ ; - | ^~~~~~~~ +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/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 /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 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 ) : - | ^~~~~~~~ +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 /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 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 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 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 /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 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 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 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/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 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 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_ ; +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 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 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 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 ) ; - | ^~~~~~~~ +In file included from ducttape.h:21, + from ducttape.cc:21: +stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 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.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + 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 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 ducttape.h:21, + from ducttape.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: + 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 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_ ; +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 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 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 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 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/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 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 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 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/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 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 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 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/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 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 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 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/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 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 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 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/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 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 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 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/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 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 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_ ; - | ^~~~~~~~ +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/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 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 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 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/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 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; | ^~~~~~~~ -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 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 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/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 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: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.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + 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 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 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/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 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; | ^~~~~~~~ -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 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 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 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; | ^~~~~~~~ @@ -2449,373 +2559,348 @@ /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 align.h:22, - from align.cc:21: +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 align_fwd.h:5, - from align.h:20, - from align.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 align.h:22, - from align.cc:21: +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 /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 /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, - from align.cc:21: +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 align_fwd.h:5, - from align.h:20, - from align.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 align.h:22, - from align.cc:21: +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.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 align.h:22, - from align.cc:21: +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.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 align.h:22, - from align.cc:21: +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.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 align.h:22, - from align.cc:21: +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.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 align.h:22, - from align.cc:21: +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.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 align.h:22, - from align.cc:21: +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.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 align.h:22, - from align.cc:21: +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.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 align.h:22, - from align.cc:21: +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.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 align.h:22, - from align.cc:21: +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.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 align.h:22, - from align.cc:21: +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.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 align.h:22, - from align.cc:21: +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.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 align.h:22, - from align.cc:21: +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.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 align.h:22, - from align.cc:21: +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.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 align.h:22, - from align.cc:21: +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from align.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 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 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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.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 stream.h:20, - from ducttape.h:21, - from ducttape.cc:21: -compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) - | ^~~~~~~~ +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.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 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, - 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_ ; +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.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 stream.h:20, - from ducttape.h:21, - from ducttape.cc:21: -compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) - | ^~~~~~~~ +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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.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 stream.h:20, - 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' -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 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/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.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 ducttape.h:21, - from ducttape.cc:21: +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_ ; @@ -2825,13 +2910,13 @@ 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: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 ) ; | ^~~~~~~~ @@ -2840,13 +2925,13 @@ 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:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -2855,13 +2940,13 @@ 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:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output | ^~~~~~~~ @@ -2870,13 +2955,13 @@ 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:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer | ^~~~~~~~ @@ -2885,13 +2970,13 @@ 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:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -2900,13 +2985,13 @@ 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 | ^~~~~~~~ @@ -2915,13 +3000,13 @@ 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 ) ; | ^~~~~~~~ @@ -2930,13 +3015,13 @@ 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:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -2945,13 +3030,13 @@ 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: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 ) : | ^~~~~~~~ @@ -2960,13 +3045,13 @@ 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:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -2975,13 +3060,13 @@ 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: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 ) : | ^~~~~~~~ @@ -2990,13 +3075,13 @@ 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:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -3005,13 +3090,13 @@ 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:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : | ^~~~~~~~ @@ -3020,13 +3105,13 @@ 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:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -3035,13 +3120,13 @@ 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: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 ) ; | ^~~~~~~~ @@ -3050,13 +3135,13 @@ 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:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; | ^~~~~~~~ @@ -3065,29 +3150,16 @@ 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.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 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; | ^~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c align.cc -o align.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence.lo sequence.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c concurrent_stream.cc -o concurrent_stream.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence.lo sequence.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c sequence.cc -fPIC -DPIC -o .libs/sequence.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c ducttape.cc -o ducttape.o >/dev/null 2>&1 In file included from stream.h:20, from sequence.cc:23: compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] @@ -3167,7 +3239,7 @@ /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/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/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c index.cc -o index.o >/dev/null 2>&1 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] @@ -3373,13 +3445,10 @@ /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/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/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c index.cc -o index.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stream.lo stream.cc +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c output_streams.cc -o output_streams.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stream.lo stream.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c stream.cc -fPIC -DPIC -o .libs/stream.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_streams.cc -o misc_streams.o >/dev/null 2>&1 -/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/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo util.cc -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo_common.cc -o anfo_common.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo util.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c util.cc -fPIC -DPIC -o .libs/util.o In file included from stream.cc:21: compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] @@ -3454,6 +3523,9 @@ /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/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/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/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c util.cc -o util.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/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c sequence.cc -o sequence.o >/dev/null 2>&1 In file included from misc_streams.h:4, from stream.cc:22: @@ -3805,7 +3877,6 @@ /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/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c util.cc -o util.o >/dev/null 2>&1 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]': @@ -3860,17 +3931,16 @@ /usr/include/google/protobuf/message_lite.h:408:7: note: declared here 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ -/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/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo-elk.lo anfo-elk.cc +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo-elk.lo anfo-elk.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo-elk.cc -fPIC -DPIC -o .libs/anfo-elk.o -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fastlz.lo fastlz.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fastlz.lo fastlz.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c fastlz.c -fPIC -DPIC -o .libs/fastlz.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c fastlz.c -o fastlz.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o config.pb.lo config.pb.cc +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o config.pb.lo config.pb.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c config.pb.cc -fPIC -DPIC -o .libs/config.pb.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o output.pb.lo output.pb.cc +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o output.pb.lo output.pb.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c output.pb.cc -fPIC -DPIC -o .libs/output.pb.o g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/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/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo-tool.o anfo-tool.cc In file included from stream.h:20, from align.h:22, from anfo_common.h:22, @@ -4372,6 +4442,63 @@ /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: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 +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 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-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() ; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +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-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 +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 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-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() ; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +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()); } + | ^~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo-tool.o anfo-tool.cc In file included from 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_ ; @@ -4445,62 +4572,6 @@ /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: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 -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 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-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() ; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -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-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 -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 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-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() ; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -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()); } - | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo.o anfo.cc g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o index-test.o index-test.cc In file included from ducttape.h:21, @@ -4882,8 +4953,8 @@ /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/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c stream.cc -o stream.o >/dev/null 2>&1 g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o file-info.o file-info.cc +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c stream.cc -o stream.o >/dev/null 2>&1 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 @@ -5848,25 +5919,25 @@ sed -e "s#__LIBDIR__#/usr/lib/aarch64-linux-gnu#g" < ./anfo.scm.in >> anfo.scm libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c output.pb.cc -o output.pb.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo-elk.cc -o anfo-elk.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libanfo.la -rpath /usr/lib/aarch64-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/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/aarch64-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/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-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/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-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/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/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/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/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/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/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/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/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/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 +/bin/sh ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fa2dna fa2dna.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt +/bin/sh ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o dnaindex dnaindex.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt +/bin/sh ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o anfo-tool anfo-tool.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt +/bin/sh ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o anfo anfo.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt +/bin/sh ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o index-test index-test.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt +/bin/sh ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o file-info file-info.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/dnaindex dnaindex.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread +libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/file-info file-info.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/anfo-tool anfo-tool.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread +libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/anfo anfo.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/fa2dna fa2dna.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread +libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/index-test index-test.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread make[4]: Leaving directory '/build/anfo-0.98/src' make[3]: Leaving directory '/build/anfo-0.98/src' Making all in man @@ -5894,7 +5965,7 @@ make[2]: Entering directory '/build/anfo-0.98' make[2]: Leaving directory '/build/anfo-0.98' make[1]: Leaving directory '/build/anfo-0.98' - rm -fr -- /tmp/dh-xdg-rundir-tpi94ous + rm -fr -- /tmp/dh-xdg-rundir-BySHor1k create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/anfo.substvars debian/libanfo0.substvars debian/libanfo0-dev.substvars @@ -5908,8 +5979,8 @@ make install-am make[3]: Entering directory '/build/anfo-0.98/src' make[4]: Entering directory '/build/anfo-0.98/src' - /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/lib/aarch64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libanfo.la '/build/anfo-0.98/debian/tmp/usr/lib/aarch64-linux-gnu' + /usr/bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/lib/aarch64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libanfo.la '/build/anfo-0.98/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libanfo.so.0.0.0 /build/anfo-0.98/debian/tmp/usr/lib/aarch64-linux-gnu/libanfo.so.0.0.0 libtool: install: (cd /build/anfo-0.98/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libanfo.so.0.0.0 libanfo.so.0 || { rm -f libanfo.so.0 && ln -s libanfo.so.0.0.0 libanfo.so.0; }; }) libtool: install: (cd /build/anfo-0.98/debian/tmp/usr/lib/aarch64-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; }; }) @@ -5918,8 +5989,8 @@ libtool: install: chmod 644 /build/anfo-0.98/debian/tmp/usr/lib/aarch64-linux-gnu/libanfo.a libtool: install: ranlib /build/anfo-0.98/debian/tmp/usr/lib/aarch64-linux-gnu/libanfo.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' - /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/bin' - /bin/bash ../libtool --mode=install /usr/bin/install -c fa2dna dnaindex anfo-tool anfo '/build/anfo-0.98/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c fa2dna dnaindex anfo-tool anfo '/build/anfo-0.98/debian/tmp/usr/bin' libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/fa2dna /build/anfo-0.98/debian/tmp/usr/bin/fa2dna libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/aarch64-linux-gnu' @@ -5928,19 +5999,19 @@ libtool: install: /usr/bin/install -c .libs/anfo-tool /build/anfo-0.98/debian/tmp/usr/bin/anfo-tool libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/anfo /build/anfo-0.98/debian/tmp/usr/bin/anfo - /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/libexec' - /bin/bash ../libtool --mode=install /usr/bin/install -c index-test file-info '/build/anfo-0.98/debian/tmp/usr/libexec' + /usr/bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/libexec' + /bin/sh ../libtool --mode=install /usr/bin/install -c index-test file-info '/build/anfo-0.98/debian/tmp/usr/libexec' libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/index-test /build/anfo-0.98/debian/tmp/usr/libexec/index-test libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/file-info /build/anfo-0.98/debian/tmp/usr/libexec/file-info - /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/anfo' + /usr/bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/anfo' /usr/bin/install -c -m 644 config.proto output.proto '/build/anfo-0.98/debian/tmp/usr/share/anfo' - /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/elk' + /usr/bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/elk' /usr/bin/install -c srfi-88.scm srfi-89.scm '/build/anfo-0.98/debian/tmp/usr/share/elk' - /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/include/anfo' + /usr/bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/include/anfo' /usr/bin/install -c -m 644 align.h align_fwd.h anfo_common.h compress_stream.h concurrent_stream.h conffile.h ducttape.h index.h logdom.h misc_streams.h output_streams.h sequence.h stream.h trim.h util.h '/build/anfo-0.98/debian/tmp/usr/include/anfo' - /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/elk' + /usr/bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/elk' /usr/bin/install -c anfo.scm '/build/anfo-0.98/debian/tmp/usr/share/elk' make[4]: Leaving directory '/build/anfo-0.98/src' make[3]: Leaving directory '/build/anfo-0.98/src' @@ -5949,15 +6020,15 @@ make[2]: Entering directory '/build/anfo-0.98/man' make[3]: Entering directory '/build/anfo-0.98/man' make[3]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/man/man1' + /usr/bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 fa2dna.1 dnaindex.1 anfo-sge.1 anfo-tool.1 file-info.1 '/build/anfo-0.98/debian/tmp/usr/share/man/man1' make[3]: Leaving directory '/build/anfo-0.98/man' make[2]: Leaving directory '/build/anfo-0.98/man' make[2]: Entering directory '/build/anfo-0.98' make[3]: Entering directory '/build/anfo-0.98' make[3]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/doc/anfo' - /bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/doc/anfo/example' + /usr/bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/doc/anfo' + /usr/bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/share/doc/anfo/example' /usr/bin/install -c -m 644 example/ancient.cfg example/default.cfg example/split-anfo.scm example/threebam.scm '/build/anfo-0.98/debian/tmp/usr/share/doc/anfo/example' /usr/bin/install -c -m 644 README '/build/anfo-0.98/debian/tmp/usr/share/doc/anfo/.' make[3]: Leaving directory '/build/anfo-0.98' @@ -6005,8 +6076,8 @@ install -p -m0644 debian/copyright debian/libanfo0-dev/usr/share/doc/libanfo0-dev/copyright dh_installchangelogs 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 + install -p -m0644 debian/changelog debian/libanfo0/usr/share/doc/libanfo0/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/anfo-0.98' @@ -6014,22 +6085,22 @@ install -p -m0644 ./debian/anfo.1 debian/anfo/usr/share/man/man1/anfo.1 man-recode --to-code UTF-8 --suffix .dh-new debian/anfo/usr/share/man/man1/anfo-sge.1 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/fa2dna.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-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/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 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.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/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/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/anfo-0.98' @@ -6044,12 +6115,12 @@ cd debian/anfo cd debian/libanfo0 cd debian/libanfo0-dev + 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-dev/changelog.Debian chmod a-x usr/share/doc/libanfo0/changelog.Debian - 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 + 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-dev/changelog.Debian gzip -9nf usr/share/doc/libanfo0/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 cd '/build/anfo-0.98' cd '/build/anfo-0.98' cd '/build/anfo-0.98' @@ -6058,22 +6129,22 @@ make[1]: Entering directory '/build/anfo-0.98' dh_fixperms 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 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s 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/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/libanfo0/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/libanfo0-dev/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/anfo/usr/share/man -type f -a -true -a -true -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/libanfo0/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libanfo0-dev/usr/include -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 -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/anfo-0.98' @@ -6147,43 +6218,43 @@ 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/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=09ff834d736da25aa3c9580235dbcdfa9f60f864 31ba71229b34a5520871b5718e4b2f1e614ee327 a1798ddc5f36fc3fe206865477f2bdc8939bf572 c3ce7798e8209207709a1e0923d3dcb79426f25a c4f3f7209c389bf98bf677f8e03917d9667edf59 c808cc3f425b921a94c51d5dc771e78854d824c5" -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=4840eb341be6f4a6d4bb2a99f8adf4f1e815ed59 -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=09ff834d736da25aa3c9580235dbcdfa9f60f864 31ba71229b34a5520871b5718e4b2f1e614ee327 a1798ddc5f36fc3fe206865477f2bdc8939bf572 c3ce7798e8209207709a1e0923d3dcb79426f25a c4f3f7209c389bf98bf677f8e03917d9667edf59 c808cc3f425b921a94c51d5dc771e78854d824c5" -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/libanfo0/DEBIAN/control + chmod 0644 -- debian/.debhelper/libanfo0/dbgsym-root/DEBIAN/control + dpkg-gencontrol -plibanfo0 -ldebian/changelog -Tdebian/libanfo0.substvars -Pdebian/libanfo0 chmod 0644 -- debian/anfo/DEBIAN/control + chmod 0644 -- debian/libanfo0/DEBIAN/control dh_md5sums - cd debian/libanfo0 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/anfo >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + cd debian/libanfo0 >/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/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/anfo/DEBIAN/md5sums + cd debian/.debhelper/anfo/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libanfo0/dbgsym-root/DEBIAN/md5sums + chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/DEBIAN/md5sums + chmod 0644 -- debian/libanfo0-dev/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: building package 'anfo' in '../anfo_0.98-8_arm64.deb'. + dpkg-deb --root-owner-group --build debian/.debhelper/anfo/dbgsym-root .. + dpkg-deb --root-owner-group --build debian/libanfo0 .. dpkg-deb: building package 'anfo-dbgsym' in '../anfo-dbgsym_0.98-8_arm64.deb'. +dpkg-deb: building package 'libanfo0-dev' in '../libanfo0-dev_0.98-8_arm64.deb'. dpkg-deb: building package 'libanfo0-dbgsym' in '../libanfo0-dbgsym_0.98-8_arm64.deb'. dpkg-deb: building package 'libanfo0' in '../libanfo0_0.98-8_arm64.deb'. -dpkg-deb: building package 'libanfo0-dev' in '../libanfo0-dev_0.98-8_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../anfo_0.98-8_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -6191,12 +6262,14 @@ 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/27766/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/27766/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/14081 and its subdirectories -I: Current time: Wed Jul 7 06:45:07 -12 2021 -I: pbuilder-time-stamp: 1625683507 +I: removing directory /srv/workspace/pbuilder/27766 and its subdirectories +I: Current time: Wed Aug 10 15:14:21 +14 2022 +I: pbuilder-time-stamp: 1660094061