Diff of the two buildlogs: -- --- b1/build.log 2021-06-18 04:29:18.595093071 +0000 +++ b2/build.log 2021-06-18 04:30:21.720717963 +0000 @@ -1,9 +1,6 @@ -W: cgroups are not available on the host, not using them. -unshare: unshare failed: Cannot allocate memory -W: pbuilder: unshare CLONE_NEWNET not available -I: pbuilder: network access is available during build! -I: Current time: Thu Jun 17 16:20:22 -12 2021 -I: pbuilder-time-stamp: 1623990022 +I: pbuilder: network access will be disabled during build +I: Current time: Fri Jul 22 00:52:19 +14 2022 +I: pbuilder-time-stamp: 1658400739 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -20,8 +17,8 @@ I: copying [./anfo_0.98-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.2dZ7fKcu/trustedkeys.kbx': General error -gpgv: Signature made Wed Nov 25 07:08:08 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.gU65RuwJ/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 @@ -37,136 +34,171 @@ 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/4051/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/32327/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-i386. +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/32327/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/32327/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-pc-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='4051' - PS1='# ' - PS2='> ' + INVOCATION_ID=0a1968b6a3ea420fbaaac6c809d2722d + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=32327 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.3RaIF70j52/pbuilderrc_IY2c --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.3RaIF70j52/b1 --logfile b1/build.log anfo_0.98-8.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/sbin/chroot' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.3RaIF70j52/pbuilderrc_tvyV --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.3RaIF70j52/b2 --logfile b2/build.log --extrapackages usrmerge anfo_0.98-8.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos2-i386 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux + Linux i-capture-the-hostname 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux I: ls -l /bin - total 5852 - -rwxr-xr-x 1 root root 1367848 Feb 24 08:57 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 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 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 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 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 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 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 210488 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 100952 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 02:38 more - -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 157996 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 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Feb 24 08:57 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jun 15 21:25 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 02:38 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 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/4051/tmp/hooks/D02_print_environment finished + total 5776 + -rwxr-xr-x 1 root root 1367848 Feb 25 2021 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 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 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 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 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 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 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 2021 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 210488 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 100952 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 2021 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 2021 more + -rwsr-xr-x 1 root root 50720 Feb 8 2021 mount + -rwxr-xr-x 1 root root 13856 Feb 8 2021 mountpoint + -rwxr-xr-x 1 root root 157996 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 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Feb 25 2021 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 22 00:52 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 20 05:46 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 2021 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 2021 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 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/32327/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -294,7 +326,7 @@ Get: 72 http://deb.debian.org/debian bullseye/main i386 libprotoc23 i386 3.12.4-1 [872 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 pkg-config i386 0.29.2-1 [66.3 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 protobuf-compiler i386 3.12.4-1 [75.3 kB] -Fetched 29.1 MB in 9s (3384 kB/s) +Fetched 29.1 MB in 0s (83.0 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 ... 19675 files and directories currently installed.) @@ -608,8 +640,44 @@ 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 i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (4729 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 ... 23030 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 +I: Running cd /build/anfo-0.98/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package anfo dpkg-buildpackage: info: source version 0.98-8 dpkg-buildpackage: info: source distribution unstable @@ -697,7 +765,7 @@ ./configure --build=i686-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/i386-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 @@ -717,10 +785,10 @@ 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 @@ -740,8 +808,8 @@ 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 @@ -848,7 +916,7 @@ config.status: executing libtool commands checking the archiver (ar) interface... ar dh_auto_build - make -j10 + make -j18 make[1]: Entering directory '/build/anfo-0.98' make all-recursive make[2]: Entering directory '/build/anfo-0.98' @@ -862,25 +930,40 @@ 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 -/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 -/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 -fPIC -DPIC -o .libs/output_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 +/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 +/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 +/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 +/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 +/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 +/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 +/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 +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 +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 +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: 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 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 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 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 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 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 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 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-elk.cc -fPIC -DPIC -o .libs/anfo-elk.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c config.pb.cc -fPIC -DPIC -o .libs/config.pb.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/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 util.cc -fPIC -DPIC -o .libs/util.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c index.cc -fPIC -DPIC -o .libs/index.o -In file included from stream.cc:21: +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 output.pb.cc -fPIC -DPIC -o .libs/output.pb.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c ducttape.cc -fPIC -DPIC -o .libs/ducttape.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 +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 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_ ; | ^~~~~~~~ @@ -888,11 +971,11 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.cc:21: +In file included from anfo-tool.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 ) | ^~~~~~~~ @@ -900,17 +983,17 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.cc:21: +In file included from anfo-tool.cc:21: compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] 198 | else if( r != Z_OK ) throw zs_.msg ; | ^~~~~~~~~~~~~ compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' -In file included from stream.cc:21: +In file included from anfo-tool.cc:21: compress_stream.h: At global scope: compress_stream.h:225:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; @@ -919,11 +1002,11 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.cc:21: +In file included from anfo-tool.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 ) | ^~~~~~~~ @@ -931,11 +1014,11 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.cc:21: +In file included from anfo-tool.cc:21: compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] 379 | else if( r < BZ_OK ) throw BzipError( r ) ; @@ -949,24 +1032,7 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: -compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)': -compress_stream.h:395:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ @@ -1066,54 +1132,53 @@ 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: + from concurrent_stream.h:23, + from concurrent_stream.cc:1: +compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)': +compress_stream.h:395:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from stream.h:20, + from concurrent_stream.h:23, + from concurrent_stream.cc:1: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from stream.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 compress_stream.h:22, + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo_common.cc:21: +In file included from stream.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 compress_stream.h:22, + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo_common.cc:21: +In file included from stream.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: +In file included from stream.cc:21: compress_stream.h: At global scope: compress_stream.h:225:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; @@ -1121,36 +1186,24 @@ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo_common.cc:21: + from compress_stream.h:22, + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo_common.cc:21: +In file included from stream.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 compress_stream.h:22, + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo_common.cc:21: +In file included from stream.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 ) ; @@ -1163,347 +1216,42 @@ In file included from /usr/include/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: 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 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: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: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from align.h:22, - from anfo_common.h:22, - from anfo_common.cc:21: -stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - 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: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 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:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo_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_ ; - | ^~~~~~~~ -In file included from /usr/include/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:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo_common.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from align.h:22, - from anfo_common.h:22, - from anfo_common.cc:21: -stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from 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: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; - | ^~~~~~~~ -In file included from align.h:22, - from anfo_common.h:22, - from anfo_common.cc:21: -stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/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:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo_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:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo_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: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: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from align.h:22, - from anfo_common.h:22, - from anfo_common.cc:21: -stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/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: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: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from align.h:22, - from anfo_common.h:22, - from anfo_common.cc:21: -stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo_common.cc:21: + from compress_stream.h:22, + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from ducttape.h:21, - from ducttape.cc:21: +In file included from index-test.cc:27: compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from ducttape.h:21, - from ducttape.cc:21: +In file included from index-test.cc:27: compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from ducttape.h:21, - from ducttape.cc:21: +In file included from index-test.cc:27: compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] 198 | else if( r != Z_OK ) throw zs_.msg ; | ^~~~~~~~~~~~~ compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' -In file included from stream.h:20, - from ducttape.h:21, - from ducttape.cc:21: +In file included from index-test.cc:27: compress_stream.h: At global scope: compress_stream.h:225:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; @@ -1511,32 +1259,24 @@ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from ducttape.h:21, - from ducttape.cc:21: +In file included from index-test.cc:27: compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from ducttape.h:21, - from ducttape.cc:21: +In file included from index-test.cc:27: compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] 379 | else if( r < BZ_OK ) throw BzipError( r ) ; @@ -1549,13 +1289,12 @@ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from index-test.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +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 stream.h:20, from output_streams.h:21, from output_streams.cc:21: @@ -1630,6 +1369,32 @@ 57 | template class auto_ptr; | ^~~~~~~~ In file included from stream.h:20, + from sequence.cc:23: +compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from sequence.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from stream.h:20, + from sequence.cc:23: +compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from sequence.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from stream.h:20, from output_streams.h:21, from output_streams.cc:21: compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': @@ -1651,8 +1416,61 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +In file included from stream.h:20, + from sequence.cc:23: +compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': +compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 198 | else if( r != Z_OK ) throw zs_.msg ; + | ^~~~~~~~~~~~~ +compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' +In file included from stream.h:20, + from sequence.cc:23: +compress_stream.h: At global scope: +compress_stream.h:225:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from sequence.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from stream.h:20, + from sequence.cc:23: +compress_stream.h: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 sequence.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from stream.h:20, + from sequence.cc:23: +compress_stream.h: 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 sequence.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h: At global scope: stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; @@ -1660,360 +1478,327 @@ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: -stream.h: At global scope: -stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: +compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: -stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: +compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: -stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: +compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': +compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 198 | else if( r != Z_OK ) throw zs_.msg ; + | ^~~~~~~~~~~~~ +compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: +compress_stream.h: At global scope: +compress_stream.h:225:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: -stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output - | ^~~~~~~~ +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: +compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: -stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer - | ^~~~~~~~ +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: +compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': +compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 379 | else if( r < BZ_OK ) throw BzipError( r ) ; + | ^~~~~~~~~~~~~~~~~~~~ +compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept' +compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)': +compress_stream.h:395:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/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 misc_streams.h:4, - from stream.cc:22: -stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: -stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from misc_streams.h:4, - from stream.cc:22: -stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ducttape.h:21, - from ducttape.cc:21: + from anfo-tool.cc:22: stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from concurrent_stream.h:23, - from concurrent_stream.cc:1: +In file included from misc_streams.h:4, + from misc_streams.cc:5: stream.h: At global scope: stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; @@ -2023,13 +1808,13 @@ 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 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 concurrent_stream.h:23, - from concurrent_stream.cc:1: +In file included from misc_streams.h:4, + from misc_streams.cc:5: stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; | ^~~~~~~~ @@ -2038,42 +1823,40 @@ 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 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 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 misc_streams.h:4, + from misc_streams.cc:5: +stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from ducttape.h:20, - from ducttape.cc:21: + from compress_stream.h:22, + from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from concurrent_stream.h:23, - from concurrent_stream.cc:1: -stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from anfo-tool.cc:22: +ducttape.h:139:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 139 | std::auto_ptr< std::ostream > out_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from concurrent_stream.h:23, - from concurrent_stream.cc:1: +In file included from misc_streams.h:4, + from misc_streams.cc:5: stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output | ^~~~~~~~ @@ -2082,99 +1865,103 @@ 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 misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from misc_streams.h:4, - from stream.cc:22: -stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + from misc_streams.cc:5: +stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from misc_streams.h:4, - from stream.cc:22: -stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : - | ^~~~~~~~ + from misc_streams.cc:5: +stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from 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 concurrent_stream.h:23, - from concurrent_stream.cc:1: -stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer +In file included from misc_streams.h:4, + from misc_streams.cc:5: +stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/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 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 concurrent_stream.h:23, - from concurrent_stream.cc:1: -stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ +In file included from misc_streams.h:4, + from misc_streams.cc:5: +stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/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 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 concurrent_stream.h:23, - from concurrent_stream.cc:1: -stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer +In file included from 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 concurrent_stream.h:23, - from concurrent_stream.cc:1: + 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 concurrent_stream.h:23, - from concurrent_stream.cc:1: -stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +In file included from 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 concurrent_stream.h:23, - from concurrent_stream.cc:1: + from misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from misc_streams.h:4, - from stream.cc:22: + 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_ ; | ^~~~~~~~ @@ -2182,12 +1969,14 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from misc_streams.h:4, - from stream.cc:22: + 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 ) : | ^~~~~~~~ @@ -2195,14 +1984,17 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: -stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +stream.h: At global scope: +stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -2214,9 +2006,9 @@ | ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: -stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : - | ^~~~~~~~ +stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -2227,8 +2019,8 @@ | ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: -stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -2239,22 +2031,39 @@ 57 | template class auto_ptr; | ^~~~~~~~ In file included from misc_streams.h:4, - from stream.cc:22: -stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; + 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.cc:21: + from stream.h:20, + from misc_streams.h:4, + from misc_streams.cc:5: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from misc_streams.h:4, from stream.cc:22: -stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; +stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -2264,143 +2073,151 @@ /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 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 concurrent_stream.h:23, - from concurrent_stream.cc:1: + 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 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 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 concurrent_stream.h:23, - from concurrent_stream.cc:1: + 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 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 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 concurrent_stream.h:23, - from concurrent_stream.cc:1: + 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 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 misc_streams.h:4, + from stream.cc:22: +stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from 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 misc_streams.h:4, + from stream.cc:22: +stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from 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 misc_streams.h:4, + from stream.cc:22: +stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer + | ^~~~~~~~ In file included from /usr/include/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 stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from 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 misc_streams.h:4, + from stream.cc:22: +stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/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 stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from 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 stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from concurrent_stream.h:23, - from concurrent_stream.cc:1: -stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; - | ^~~~~~~~ +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from stream.h:20, - from sequence.cc:23: + from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': +compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 198 | else if( r != Z_OK ) throw zs_.msg ; + | ^~~~~~~~~~~~~ +compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' +In file included from stream.h:20, + from align.h:22, + from align.cc:21: compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -2408,12 +2225,15 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from sequence.cc:21: + from align_fwd.h:5, + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from stream.h:20, - from sequence.cc:23: + from align.h:22, + from align.cc:21: compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) | ^~~~~~~~ @@ -2421,19 +2241,84 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from sequence.cc:21: + from align_fwd.h:5, + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from stream.h:20, - from sequence.cc:23: + from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +compress_stream.h: At global scope: +compress_stream.h:225:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from stream.h:20, + from align.h:22, + from align.cc:21: compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] 198 | else if( r != Z_OK ) throw zs_.msg ; | ^~~~~~~~~~~~~ compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' In file included from stream.h:20, - from sequence.cc:23: + from align.h:22, + from anfo_common.h:22, + from anfo.cc:21: +compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': +compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 379 | else if( r < BZ_OK ) throw BzipError( r ) ; + | ^~~~~~~~~~~~~~~~~~~~ +compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept' +compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)': +compress_stream.h:395:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from stream.h:20, + from align.h:22, + from align.cc:21: compress_stream.h: At global scope: compress_stream.h:225:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; @@ -2442,12 +2327,15 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from sequence.cc:21: + from align_fwd.h:5, + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from stream.h:20, - from sequence.cc:23: + from align.h:22, + from align.cc:21: compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) | ^~~~~~~~ @@ -2455,26 +2343,67 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from sequence.cc:21: + from align_fwd.h:5, + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -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 misc_streams.h:4, + from stream.cc:22: +stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from concurrent_stream.h:23, - from concurrent_stream.cc:1: + from stream.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from misc_streams.h:4, + from stream.cc:22: +stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from stream.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from misc_streams.h:4, + from stream.cc:22: +stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from stream.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from misc_streams.h:4, + from stream.cc:22: +stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from stream.h:20, - from sequence.cc:23: + from align.h:22, + from align.cc:21: compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] 379 | else if( r < BZ_OK ) throw BzipError( r ) ; @@ -2488,89 +2417,143 @@ from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, - from sequence.cc:21: + from align_fwd.h:5, + from align.h:20, + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -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 misc_streams.h:4, + from stream.cc:22: +stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/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 stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: +In file included from misc_streams.h:4, + from stream.cc:22: +stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 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.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from misc_streams.h:4, + from stream.cc:22: +stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from stream.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from misc_streams.h:4, + from stream.cc:22: +stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from stream.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from misc_streams.h:4, + from stream.cc:22: +stream.h: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.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: At global scope: stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from 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: +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/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: +In file included from concurrent_stream.h:23, + from concurrent_stream.cc:1: stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /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: +In file included from concurrent_stream.h:23, + from concurrent_stream.cc:1: stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output | ^~~~~~~~ In file included from /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:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer +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, @@ -2584,9 +2567,9 @@ | ^~~~~~~~ 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_ ; - | ^~~~~~~~ +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, @@ -2599,8 +2582,8 @@ | ^~~~~~~~ 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 +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, @@ -2612,25 +2595,25 @@ /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:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from 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:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +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, @@ -2642,115 +2625,104 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.h:21, - from output_streams.cc:21: -stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : - | ^~~~~~~~ +In file included from concurrent_stream.h:23, + from concurrent_stream.cc:1: +stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /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: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 concurrent_stream.h:23, + from concurrent_stream.cc:1: +stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer | ^~~~~~~~ In file included from /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: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 sequence.cc:23: +stream.h: At global scope: +stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.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 sequence.cc:23: +stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.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 concurrent_stream.h:23, + from concurrent_stream.cc:1: +stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/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: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 sequence.cc:23: +stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.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 sequence.cc:23: +stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from output_streams.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_ ; +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, @@ -2762,10 +2734,11 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.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 output_streams.h:21, + from output_streams.cc:21: +stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/coded_stream.h:141, @@ -2776,9 +2749,10 @@ /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 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, @@ -2790,10 +2764,11 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.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 output_streams.h:21, + from output_streams.cc:21: +stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/coded_stream.h:141, @@ -2804,129 +2779,106 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.cc:21: -output_streams.h:138:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 138 | std::auto_ptr< std::ostream > out_ ; +In file included from sequence.cc:23: +stream.h: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 sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.cc:21: -output_streams.h:149:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 149 | std::auto_ptr< std::ostream > out_ ; +In file included from sequence.cc:23: +stream.h: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 sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from output_streams.cc:21: -output_streams.h:176:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 176 | std::auto_ptr< std::ostream > out_ ; +In file included from sequence.cc:23: +stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/coded_stream.h:141, - from config.pb.h:23, - from index.h:20, - from output_streams.h:20, - from output_streams.cc:21: + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -stream.cc:81:30: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 81 | AnfoReader::AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name ) - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: -stream.h: At global scope: -stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from 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 sequence.h:30, - from sequence.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 sequence.cc:23: -stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +In file included from 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 sequence.h:30, - from sequence.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; | ^~~~~~~~ -stream.cc: In member function 'virtual void streams::ChunkedWriter::put_result(const output::Result&)': -stream.cc:344:27: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] - 344 | flush_buffer( r.ByteSize() ) ; - | ^ In file included from stream.h:20, from align.h:22, - from align.cc:21: + 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 /usr/include/google/protobuf/generated_enum_util.h:36, - from /usr/include/google/protobuf/map.h:49, - from /usr/include/google/protobuf/generated_message_table_driven.h:34, - from output.pb.h:26, - from stream.h:22, - from misc_streams.h:4, - from stream.cc:22: -/usr/include/google/protobuf/message_lite.h:408:7: note: declared here - 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } - | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, from align.h:20, - from align.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from sequence.cc:23: -stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from sequence.cc:21: + 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 stream.h:20, from align.h:22, - from align.cc:21: + from anfo_common.h:22, + from anfo_common.cc:21: compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) | ^~~~~~~~ @@ -2936,82 +2888,117 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from align.cc:21: + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: -stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output +In file included from 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 /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from sequence.cc:21: + from compress_stream.h:22, + from stream.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; | ^~~~~~~~ -stream.cc: At global scope: -stream.cc:421:36: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 421 | ChunkedReader::ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name ) - | ^~~~~~~~ +In file included from 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 /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.cc:21: + from stream.h:20, + from concurrent_stream.h:23, + from concurrent_stream.cc:1: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from align.cc:21: -compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': -compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 198 | else if( r != Z_OK ) throw zs_.msg ; - | ^~~~~~~~~~~~~ -compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' -In file included from sequence.cc:23: -stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer +In file included from 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 sequence.cc:21: + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: -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 output_streams.h:21, + from output_streams.cc:21: +stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from 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 /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from sequence.cc:21: + from compress_stream.h:22, + from stream.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: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 sequence.cc:23: -stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer +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 /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from sequence.cc:23: -stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ +stream.h: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, @@ -3022,7 +3009,47 @@ | ^~~~~~~~ In file included from stream.h:20, from align.h:22, - from align.cc:21: + from anfo_common.h:22, + from anfo_common.cc:21: +compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': +compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 198 | else if( r != Z_OK ) throw zs_.msg ; + | ^~~~~~~~~~~~~ +compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' +In file included from 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 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: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: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: compress_stream.h: At global scope: compress_stream.h:225:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; @@ -3033,13 +3060,15 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from align.cc:21: + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from stream.h:20, from align.h:22, - from align.cc:21: + from anfo_common.h:22, + from anfo_common.cc:21: compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) | ^~~~~~~~ @@ -3049,53 +3078,53 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from align.cc:21: + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from align.cc:21: -compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': -compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 379 | else if( r < BZ_OK ) throw BzipError( r ) ; - | ^~~~~~~~~~~~~~~~~~~~ -compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept' -compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)': -compress_stream.h:395:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( - | ^~~~~~~~ +In file included from 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 sequence.cc:23: -stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ +In file included from 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 sequence.cc:21: + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: -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: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 sequence.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; | ^~~~~~~~ @@ -3123,33 +3152,39 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: +In file included from output_streams.h:21, + from output_streams.cc:21: stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from sequence.cc:21: + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: +In file included from output_streams.h:21, + from output_streams.cc:21: stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from sequence.cc:21: + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from sequence.cc:23: -stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +stream.h: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, @@ -3160,8 +3195,8 @@ 57 | template class auto_ptr; | ^~~~~~~~ In file included from sequence.cc:23: -stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; +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, @@ -3171,111 +3206,128 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from sequence.cc:23: -stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; +In file included from 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 sequence.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -stream.cc:1093:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1093 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -stream.cc:1114:29: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1114 | StreamWithProgress( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, int64_t total ) - | ^~~~~~~~ +In file included from 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 compress_stream.h:22, - from stream.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; | ^~~~~~~~ -stream.cc:1149:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1149 | StreamHolder make_input_stream_( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, bool solexa_scores, char origin, const string& genome ) - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -stream.cc: In function 'streams::StreamHolder streams::{anonymous}::make_input_stream_(std::auto_ptr, const string&, bool, char, const string&)': -stream.cc:1179:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1179 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > bs( new BunzipStream( is ) ) ; - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -stream.cc:1189:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1189 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > zs( new InflateStream( is ) ) ; - | ^~~~~~~~ +In file included from stream.h:20, + from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: +compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': +compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] + 379 | else if( r < BZ_OK ) throw BzipError( r ) ; + | ^~~~~~~~~~~~~~~~~~~~ +compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept' +compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)': +compress_stream.h:395:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -stream.cc: In member function 'virtual output::Header streams::UniversalReader::fetch_header()': -stream.cc:1233:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1233 | std::auto_ptr< google::protobuf::io::FileInputStream > s( new google::protobuf::io::FileInputStream( fd ) ) ; - | ^~~~~~~~ +In file included from 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 compress_stream.h:22, - from stream.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; | ^~~~~~~~ -stream.cc:1238:12: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1238 | std::auto_ptr(s), name_, st.st_size ) ) ; - | ^~~~~~~~ +In file included from sequence.cc:23: +stream.h: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.cc:21: + from sequence.h:30, + from sequence.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -stream.cc: At global scope: -stream.cc:1378:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 1378 | BamReader::BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) : - | ^~~~~~~~ +In file included from 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/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.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 misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h: At global scope: stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; @@ -3283,255 +3335,398 @@ In file included from /usr/include/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-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; | ^~~~~~~~ In file included from /usr/include/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-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output | ^~~~~~~~ In file included from /usr/include/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-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from output_streams.cc:21: +output_streams.h:72:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 72 | std::auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo-elk.cc:27: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +concurrent_stream.cc: In member function 'virtual output::Result streams::ConcurrentStream::fetch_result()': +concurrent_stream.cc:178:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 178 | auto_ptr< Result > r( outgoing_[ next_out_++ ] ) ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, from stream.h:20, - from 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 align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/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-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo-elk.cc:27: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +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; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from output_streams.cc:21: +output_streams.h:123:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 123 | std::auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.cc:21: +output_streams.h:138:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 138 | std::auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.cc:21: +output_streams.h:149:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 149 | std::auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from output_streams.cc:21: +output_streams.h:176:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 176 | std::auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/coded_stream.h:141, + from config.pb.h:23, + from index.h:20, + from output_streams.h:20, + from output_streams.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/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-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : | ^~~~~~~~ In file included from /usr/include/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-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 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: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 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: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/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-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : | ^~~~~~~~ In file included from /usr/include/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-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/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-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; | ^~~~~~~~ In file included from /usr/include/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-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from misc_streams.h:4, - from misc_streams.cc:5: +In file included from align.h:22, + from anfo_common.h:22, + from anfo-elk.cc:27: stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo-elk.cc:27: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +stream.cc:81:30: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 81 | AnfoReader::AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name ) + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from stream.h:20, - from misc_streams.h:4, - from misc_streams.cc:5: + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from align.cc:21: + from anfo_common.h:22, + from anfo.cc:21: stream.h: At global scope: stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; @@ -3542,12 +3737,14 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from align.cc:21: + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from align.cc:21: + from anfo_common.h:22, + from anfo.cc:21: stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; | ^~~~~~~~ @@ -3557,12 +3754,14 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from align.cc:21: + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from align.cc:21: + from anfo_common.h:22, + from anfo.cc:21: stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ @@ -3572,12 +3771,14 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from align.cc:21: + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from align.cc:21: + from anfo_common.h:22, + from anfo.cc:21: stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output | ^~~~~~~~ @@ -3587,14 +3788,16 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from align.cc:21: + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from 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 +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, @@ -3608,9 +3811,9 @@ | ^~~~~~~~ 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_ ; - | ^~~~~~~~ +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, @@ -3622,9 +3825,10 @@ 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from align.cc:21: -stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer + from anfo_common.h:22, + from anfo.cc:21: +stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -3632,15 +3836,16 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from align.cc:21: + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from 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 ) ; - | ^~~~~~~~ +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, @@ -3652,9 +3857,10 @@ 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from align.cc:21: -stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + from anfo_common.h:22, + from anfo.cc:21: +stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -3662,45 +3868,50 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from align.cc:21: + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from 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 ) : - | ^~~~~~~~ + from anfo_common.h:22, + from anfo.cc:21: +stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, from align.h:20, - from align.cc:21: + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from 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_ ; - | ^~~~~~~~ + from anfo_common.h:22, + from anfo.cc:21: +stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, from align.h:20, - from align.cc:21: + from anfo_common.h:22, + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from 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 ) : - | ^~~~~~~~ +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, @@ -3713,8 +3924,8 @@ | ^~~~~~~~ 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_ ; +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, @@ -3728,9 +3939,9 @@ | ^~~~~~~~ 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 ) : - | ^~~~~~~~ +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, @@ -3743,8 +3954,8 @@ | ^~~~~~~~ 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_ ; +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, @@ -3758,9 +3969,9 @@ | ^~~~~~~~ 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 ) ; - | ^~~~~~~~ +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, @@ -3771,125 +3982,42 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from align.cc:21: -stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; +In file included from stream.h:20, + from 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 align.cc:21: -/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: + 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 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]': -stream.h:102:25: required from 'void streams::write_delimited_message(google::protobuf::io::ZeroCopyOutputStream*, int, const Msg&) [with Msg = output::Header]' -stream.cc:322:44: required from here -stream.h:88:30: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] - 88 | os.WriteVarint32( m.ByteSize() ) ; - | ~~~~~~~~~~^~ -In file included from /usr/include/google/protobuf/generated_enum_util.h:36, - from /usr/include/google/protobuf/map.h:49, - from /usr/include/google/protobuf/generated_message_table_driven.h:34, - from output.pb.h:26, - from stream.h:22, - from misc_streams.h:4, - from stream.cc:22: -/usr/include/google/protobuf/message_lite.h:408:7: note: declared here - 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } - | ^~~~~~~~ -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::Footer]': -stream.h:102:25: required from 'void streams::write_delimited_message(google::protobuf::io::ZeroCopyOutputStream*, int, const Msg&) [with Msg = output::Footer]' -stream.cc:331:44: required from here -stream.h:88:30: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] - 88 | os.WriteVarint32( m.ByteSize() ) ; - | ~~~~~~~~~~^~ -In file included from /usr/include/google/protobuf/generated_enum_util.h:36, - from /usr/include/google/protobuf/map.h:49, - from /usr/include/google/protobuf/generated_message_table_driven.h:34, - from output.pb.h:26, - from stream.h:22, - from misc_streams.h:4, - from stream.cc:22: -/usr/include/google/protobuf/message_lite.h:408:7: note: declared here - 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } - | ^~~~~~~~ -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::Result]': -stream.h:102:25: required from 'void streams::write_delimited_message(google::protobuf::io::ZeroCopyOutputStream*, int, const Msg&) [with Msg = output::Result]' -stream.cc:345:44: required from here -stream.h:88:30: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] - 88 | os.WriteVarint32( m.ByteSize() ) ; - | ~~~~~~~~~~^~ -In file included from /usr/include/google/protobuf/generated_enum_util.h:36, - from /usr/include/google/protobuf/map.h:49, - from /usr/include/google/protobuf/generated_message_table_driven.h:34, - from output.pb.h:26, - from stream.h:22, - from misc_streams.h:4, - from stream.cc:22: -/usr/include/google/protobuf/message_lite.h:408:7: note: declared here - 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } - | ^~~~~~~~ -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 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 -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 -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 -/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 -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 anfo-elk.cc -fPIC -DPIC -o .libs/anfo-elk.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/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 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 stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: -compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ + 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-elk.cc:27: + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: -compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) - | ^~~~~~~~ +In file included from anfo-elk.cc:28: +ducttape.h:139:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 139 | std::auto_ptr< std::ostream > out_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -3902,18 +4030,16 @@ 57 | template class auto_ptr; | ^~~~~~~~ In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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 align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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_ ; @@ -3923,19 +4049,17 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, +In file included from align.h:22, from anfo_common.h:22, - from anfo-elk.cc:27: -compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) - | ^~~~~~~~ + from anfo.cc:21: +stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -3943,41 +4067,32 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from stream.h:20, - from align.h:22, + from 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 align.h:22, from anfo_common.h:22, - from anfo-elk.cc:27: -compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': -compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 379 | else if( r < BZ_OK ) throw BzipError( r ) ; - | ^~~~~~~~~~~~~~~~~~~~ -compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept' -compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)': -compress_stream.h:395:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( - | ^~~~~~~~ + from anfo.cc:21: +stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h: At global scope: -stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -3985,16 +4100,30 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +stream.cc: In member function 'virtual void streams::ChunkedWriter::put_result(const output::Result&)': +stream.cc:344:27: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] + 344 | flush_buffer( r.ByteSize() ) ; + | ^ +In file included from /usr/include/google/protobuf/generated_enum_util.h:36, + from /usr/include/google/protobuf/map.h:49, + from /usr/include/google/protobuf/generated_message_table_driven.h:34, + from output.pb.h:26, + from stream.h:22, + from misc_streams.h:4, + from stream.cc:22: +/usr/include/google/protobuf/message_lite.h:408:7: note: declared here + 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } + | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:323:20: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ + from anfo.cc:21: +stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -4002,16 +4131,30 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + from anfo.cc:21: /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 align.h:22, from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ + from anfo.cc:21: +stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from stream.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 /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -4019,32 +4162,36 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output - | ^~~~~~~~ +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-elk.cc:27: + from ducttape.h:20, + from ducttape.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:387:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer + from align.cc:21: +stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -4052,33 +4199,42 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from align.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +stream.cc: At global scope: +stream.cc:421:36: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 421 | ChunkedReader::ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name ) + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:414:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ + from align.cc:21: +stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:416:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer + from anfo.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, @@ -4087,16 +4243,16 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; - | ^~~~~~~~ + from anfo.cc:21: +stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -4104,16 +4260,15 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -/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 In file included from align.h:22, from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + from anfo.cc:21: +stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, @@ -4122,16 +4277,16 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo-elk.cc:27: -stream.h:762:21: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) : - | ^~~~~~~~ + from anfo.cc:21: +stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, @@ -4139,13 +4294,12 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo-elk.cc:27: + from anfo.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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_ ; | ^~~~~~~~ @@ -4155,14 +4309,12 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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 ) : | ^~~~~~~~ @@ -4172,14 +4324,29 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, from anfo_common.h:22, - from anfo-elk.cc:27: + from anfo.cc:21: +stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from 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_ ; | ^~~~~~~~ @@ -4189,14 +4356,12 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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 ) : | ^~~~~~~~ @@ -4206,14 +4371,12 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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_ ; | ^~~~~~~~ @@ -4223,14 +4386,12 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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 ) ; | ^~~~~~~~ @@ -4240,14 +4401,12 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from align.h:22, - from anfo_common.h:22, - from anfo-elk.cc:27: + 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_ ; | ^~~~~~~~ @@ -4257,259 +4416,164 @@ from sequence.h:30, from align_fwd.h:5, from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from anfo-elk.cc:28: -ducttape.h:139:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 139 | std::auto_ptr< std::ostream > out_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from align.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -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: 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 config.pb.lo config.pb.cc -In file included from anfo-elk.cc:31: +In file included from anfo-tool.cc:24: output_streams.h:45:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 45 | auto_ptr< std::ostream > out_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-elk.cc:31: +In file included from anfo-tool.cc:24: output_streams.h:72:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 72 | std::auto_ptr< std::ostream > out_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-elk.cc:31: +In file included from anfo-tool.cc:24: output_streams.h:123:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 123 | std::auto_ptr< std::ostream > out_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-elk.cc:31: +In file included from anfo-tool.cc:24: output_streams.h:138:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 138 | std::auto_ptr< std::ostream > out_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-elk.cc:31: +In file included from anfo-tool.cc:24: output_streams.h:149:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 149 | std::auto_ptr< std::ostream > out_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from compress_stream.h:22, + from anfo-tool.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-elk.cc:31: +In file included from anfo-tool.cc:24: output_streams.h:176:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 176 | std::auto_ptr< std::ostream > out_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from sequence.h:30, - from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo-elk.cc:27: + from compress_stream.h:22, + from anfo-tool.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 config.pb.cc -fPIC -DPIC -o .libs/config.pb.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo_common.cc -o anfo_common.o >/dev/null 2>&1 -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()); } - | ^~~~~~~~~ -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 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 -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 anfo-tool.o anfo-tool.cc -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/anfo-0.98=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo.o anfo.cc -In file included from anfo-tool.cc:21: -compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ +stream.cc:1093:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1093 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from anfo-tool.cc:21: + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-tool.cc:21: -compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) - | ^~~~~~~~ +stream.cc:1114:29: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1114 | StreamWithProgress( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, int64_t total ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from anfo-tool.cc:21: + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-tool.cc:21: -compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': -compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 198 | else if( r != Z_OK ) throw zs_.msg ; - | ^~~~~~~~~~~~~ -compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' -In file included from anfo-tool.cc:21: -compress_stream.h: At global scope: -compress_stream.h:225:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ +stream.cc:1149:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1149 | StreamHolder make_input_stream_( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, bool solexa_scores, char origin, const string& genome ) + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from anfo-tool.cc:21: + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-tool.cc:21: -compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) - | ^~~~~~~~ +stream.cc: In function 'streams::StreamHolder streams::{anonymous}::make_input_stream_(std::auto_ptr, const string&, bool, char, const string&)': +stream.cc:1179:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1179 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > bs( new BunzipStream( is ) ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from anfo-tool.cc:21: + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-tool.cc:21: -compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': -compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 379 | else if( r < BZ_OK ) throw BzipError( r ) ; - | ^~~~~~~~~~~~~~~~~~~~ -compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept' -compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)': -compress_stream.h:395:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( - | ^~~~~~~~ +stream.cc:1189:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1189 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > zs( new InflateStream( is ) ) ; + | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from anfo-tool.cc:21: + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: +stream.cc: In member function 'virtual output::Header streams::UniversalReader::fetch_header()': +stream.cc:1233:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1233 | std::auto_ptr< google::protobuf::io::FileInputStream > s( new google::protobuf::io::FileInputStream( fd ) ) ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from stream.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +stream.cc:1238:12: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1238 | std::auto_ptr(s), name_, st.st_size ) ) ; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from compress_stream.h:22, + from stream.cc:21: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from align.h:22, + from anfo_common.h:22, + from anfo_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_ ; @@ -4517,382 +4581,332 @@ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: +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 /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: stream.h:345:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: stream.h:385:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, + from sequence.h:30, + from align_fwd.h:5, + from 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; + | ^~~~~~~~ +stream.cc: At global scope: +stream.cc:1378:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] + 1378 | BamReader::BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) : + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /usr/include/google/protobuf/stubs/common.h:41, + from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from compress_stream.h:22, - from anfo-tool.cc:21: + from stream.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: +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/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: +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 anfo-tool.cc:21: + 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 ducttape.h:21, - from anfo-tool.cc:22: +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 anfo-tool.cc:21: + 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 ducttape.h:21, - from anfo-tool.cc:22: +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: stream.h:422:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + 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 ducttape.h:21, - from anfo-tool.cc:22: +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + 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 ducttape.h:21, - from anfo-tool.cc:22: +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 compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: stream.h:772:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: stream.h:795:19: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) : | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: stream.h:806:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: stream.h:821:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) : | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: stream.h:832:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: stream.h:846:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo_common.cc:21: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from ducttape.h:21, - from anfo-tool.cc:22: +In file included from align.h:22, + from anfo_common.h:22, + from anfo_common.cc:21: stream.h:880:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from anfo-tool.cc:22: -ducttape.h:139:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 139 | std::auto_ptr< std::ostream > out_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + 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; | ^~~~~~~~ -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 anfo-tool.cc:24: +In file included from anfo-elk.cc:31: output_streams.h:45:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 45 | auto_ptr< std::ostream > out_ ; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/google/protobuf/stubs/common.h:41, from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: + from sequence.h:30, + from align_fwd.h:5, + from align.h:20, + from anfo_common.h:22, + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from anfo-tool.cc:24: +In file included from anfo-elk.cc:31: 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 compress_stream.h:22, - from anfo-tool.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from anfo-tool.cc:24: -output_streams.h:123:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 123 | std::auto_ptr< std::ostream > out_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from anfo-tool.cc:24: -output_streams.h:138:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 138 | std::auto_ptr< std::ostream > out_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from anfo-tool.cc:24: -output_streams.h:149:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 149 | std::auto_ptr< std::ostream > out_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from anfo-tool.cc:24: -output_streams.h:176:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 176 | std::auto_ptr< std::ostream > out_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from anfo-tool.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -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 -In file included from anfo-tool.cc:23: -misc_streams.h: In instantiation of 'void streams::SortingStream::put_result(const output::Result&) [with Comp = streams::by_seqid]': -misc_streams.h:282:16: required from here -misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] - 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -In file included from output.pb.h:31, - from sequence.h:32, - from align_fwd.h:5, - from ducttape.h:20, - from anfo-tool.cc:22: -/usr/include/google/protobuf/message.h:299:7: note: declared here - 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } - | ^~~~~~~~~ -In file included from anfo-tool.cc:23: -misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] - 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -In file included from output.pb.h:31, - from sequence.h:32, - from align_fwd.h:5, - from ducttape.h:20, - from anfo-tool.cc:22: -/usr/include/google/protobuf/message.h:299:7: note: declared here - 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } - | ^~~~~~~~~ -In file included from anfo-tool.cc:23: -misc_streams.h: In instantiation of 'void streams::SortingStream::put_result(const output::Result&) [with Comp = streams::by_genome_coordinate]': -misc_streams.h:282:16: required from here -misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] - 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -In file included from output.pb.h:31, - from sequence.h:32, - from align_fwd.h:5, - from ducttape.h:20, - from anfo-tool.cc:22: -/usr/include/google/protobuf/message.h:299:7: note: declared here - 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } - | ^~~~~~~~~ -In file included from anfo-tool.cc:23: -misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] - 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -In file included from output.pb.h:31, - from sequence.h:32, - from align_fwd.h:5, - from ducttape.h:20, - from anfo-tool.cc:22: -/usr/include/google/protobuf/message.h:299:7: note: declared here - 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } - | ^~~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: -compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: -compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) - | ^~~~~~~~ +In file included from anfo-elk.cc:31: +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, @@ -4900,26 +4914,13 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: -compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': -compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 198 | else if( r != Z_OK ) throw zs_.msg ; - | ^~~~~~~~~~~~~ -compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: -compress_stream.h: At global scope: -compress_stream.h:225:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from anfo-elk.cc:31: +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, @@ -4928,17 +4929,14 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: -compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) - | ^~~~~~~~ +In file included from anfo-elk.cc:31: +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, @@ -4946,23 +4944,14 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from stream.h:20, - from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: -compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': -compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 379 | else if( r < BZ_OK ) throw BzipError( r ) ; - | ^~~~~~~~~~~~~~~~~~~~ -compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept' -compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)': -compress_stream.h:395:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( - | ^~~~~~~~ +In file included from anfo-elk.cc:31: +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, @@ -4970,13 +4959,12 @@ from align_fwd.h:5, from align.h:20, from anfo_common.h:22, - from anfo.cc:21: + from anfo-elk.cc:27: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from align.h:22, - from anfo_common.h:22, - from anfo.cc:21: +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_ ; @@ -4986,15 +4974,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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 ) ; | ^~~~~~~~ @@ -5003,15 +4989,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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_ ; | ^~~~~~~~ @@ -5020,15 +5004,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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 | ^~~~~~~~ @@ -5037,15 +5019,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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 | ^~~~~~~~ @@ -5054,15 +5034,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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_ ; | ^~~~~~~~ @@ -5071,15 +5049,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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 | ^~~~~~~~ @@ -5088,15 +5064,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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 ) ; | ^~~~~~~~ @@ -5105,15 +5079,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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_ ; | ^~~~~~~~ @@ -5122,15 +5094,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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 ) : | ^~~~~~~~ @@ -5139,15 +5109,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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_ ; | ^~~~~~~~ @@ -5156,15 +5124,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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 ) : | ^~~~~~~~ @@ -5173,15 +5139,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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_ ; | ^~~~~~~~ @@ -5190,15 +5154,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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 ) : | ^~~~~~~~ @@ -5207,15 +5169,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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_ ; | ^~~~~~~~ @@ -5224,15 +5184,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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 ) ; | ^~~~~~~~ @@ -5241,15 +5199,13 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: + from 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.cc:21: +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_ ; | ^~~~~~~~ @@ -5258,87 +5214,79 @@ from /usr/include/google/protobuf/io/zero_copy_stream.h:113, from sequence.h:30, from align_fwd.h:5, - from align.h:20, - from anfo_common.h:22, - from anfo.cc:21: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from index-test.cc:27: -compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from index-test.cc:27: -compress_stream.h:97:23: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 ) - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: + 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 index-test.cc:27: -compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()': -compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 198 | else if( r != Z_OK ) throw zs_.msg ; - | ^~~~~~~~~~~~~ -compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept' -In file included from index-test.cc:27: -compress_stream.h: At global scope: -compress_stream.h:225:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; +In file included from 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 index-test.cc:27: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from index-test.cc:27: -compress_stream.h:278:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ) - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: + from sequence.h:30, + from align_fwd.h:5, + from 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 index-test.cc:27: -compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()': -compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate] - 379 | else if( r < BZ_OK ) throw BzipError( r ) ; - | ^~~~~~~~~~~~~~~~~~~~ -compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept' -compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)': -compress_stream.h:395:7: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] - 395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos( +In file included from 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]': +stream.h:102:25: required from 'void streams::write_delimited_message(google::protobuf::io::ZeroCopyOutputStream*, int, const Msg&) [with Msg = output::Header]' +stream.cc:322:44: required from here +stream.h:88:30: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] + 88 | os.WriteVarint32( m.ByteSize() ) ; + | ~~~~~~~~~~^~ +In file included from /usr/include/google/protobuf/generated_enum_util.h:36, + from /usr/include/google/protobuf/map.h:49, + from /usr/include/google/protobuf/generated_message_table_driven.h:34, + from output.pb.h:26, + from stream.h:22, + from misc_streams.h:4, + from stream.cc:22: +/usr/include/google/protobuf/message_lite.h:408:7: note: declared here + 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } + | ^~~~~~~~ +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::Footer]': +stream.h:102:25: required from 'void streams::write_delimited_message(google::protobuf::io::ZeroCopyOutputStream*, int, const Msg&) [with Msg = output::Footer]' +stream.cc:331:44: required from here +stream.h:88:30: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] + 88 | os.WriteVarint32( m.ByteSize() ) ; + | ~~~~~~~~~~^~ +In file included from /usr/include/google/protobuf/generated_enum_util.h:36, + from /usr/include/google/protobuf/map.h:49, + from /usr/include/google/protobuf/generated_message_table_driven.h:34, + from output.pb.h:26, + from stream.h:22, + from misc_streams.h:4, + from stream.cc:22: +/usr/include/google/protobuf/message_lite.h:408:7: note: declared here + 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } + | ^~~~~~~~ +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::Result]': +stream.h:102:25: required from 'void streams::write_delimited_message(google::protobuf::io::ZeroCopyOutputStream*, int, const Msg&) [with Msg = output::Result]' +stream.cc:345:44: required from here +stream.h:88:30: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] + 88 | os.WriteVarint32( m.ByteSize() ) ; + | ~~~~~~~~~~^~ +In file included from /usr/include/google/protobuf/generated_enum_util.h:36, + from /usr/include/google/protobuf/map.h:49, + from /usr/include/google/protobuf/generated_message_table_driven.h:34, + from output.pb.h:26, + from stream.h:22, + from misc_streams.h:4, + from stream.cc:22: +/usr/include/google/protobuf/message_lite.h:408:7: note: declared here + 408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /usr/include/google/protobuf/stubs/common.h:41, - from /usr/include/google/protobuf/io/zero_copy_stream.h:113, - from compress_stream.h:22, - from index-test.cc:27: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -echo "; DO NOT EDIT THIS FILE! EDIT anfo.scm.in AND RUN MAKE INSTEAD!" > anfo.scm -sed -e "s#__LIBDIR__#/usr/lib/i386-linux-gnu#g" < ./anfo.scm.in >> anfo.scm In file included from index-test.cc:30: stream.h: At global scope: stream.h:319:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] @@ -5436,6 +5384,58 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +In file included from anfo-tool.cc:23: +misc_streams.h: In instantiation of 'void streams::SortingStream::put_result(const output::Result&) [with Comp = streams::by_seqid]': +misc_streams.h:282:16: required from here +misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] + 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +In file included from output.pb.h:31, + from sequence.h:32, + from align_fwd.h:5, + from ducttape.h:20, + from anfo-tool.cc:22: +/usr/include/google/protobuf/message.h:299:7: note: declared here + 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } + | ^~~~~~~~~ +In file included from anfo-tool.cc:23: +misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] + 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +In file included from output.pb.h:31, + from sequence.h:32, + from align_fwd.h:5, + from ducttape.h:20, + from anfo-tool.cc:22: +/usr/include/google/protobuf/message.h:299:7: note: declared here + 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } + | ^~~~~~~~~ +In file included from anfo-tool.cc:23: +misc_streams.h: In instantiation of 'void streams::SortingStream::put_result(const output::Result&) [with Comp = streams::by_genome_coordinate]': +misc_streams.h:282:16: required from here +misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] + 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +In file included from output.pb.h:31, + from sequence.h:32, + from align_fwd.h:5, + from ducttape.h:20, + from anfo-tool.cc:22: +/usr/include/google/protobuf/message.h:299:7: note: declared here + 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } + | ^~~~~~~~~ +In file included from anfo-tool.cc:23: +misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations] + 284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +In file included from output.pb.h:31, + from sequence.h:32, + from align_fwd.h:5, + from ducttape.h:20, + from anfo-tool.cc:22: +/usr/include/google/protobuf/message.h:299:7: note: declared here + 299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); } + | ^~~~~~~~~ In file included from index-test.cc:30: stream.h:747:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ; @@ -5544,6 +5544,68 @@ /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()); } + | ^~~~~~~~~ +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 +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 concurrent_stream.cc -o concurrent_stream.o >/dev/null 2>&1 +echo "; DO NOT EDIT THIS FILE! EDIT anfo.scm.in AND RUN MAKE INSTEAD!" > anfo.scm +sed -e "s#__LIBDIR__#/usr/lib/i386-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 sequence.cc -o sequence.o >/dev/null 2>&1 In file included from stream.h:20, from file-info.cc:25: compress_stream.h:34:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] @@ -5850,28 +5912,34 @@ /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 +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 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 config.pb.cc -o config.pb.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/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 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 stream.cc -o stream.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/build/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/i386-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/i386-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/i686-linux-gnu/10/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-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/i686-linux-gnu/10 -L/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/10/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/10/crtendS.o /usr/lib/gcc/i686-linux-gnu/10/../../../i386-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 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 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 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 file-info file-info.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 -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 +/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/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/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/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 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/anfo-tool anfo-tool.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 @@ -5883,7 +5951,7 @@ make[2]: Leaving directory '/build/anfo-0.98' make[1]: Leaving directory '/build/anfo-0.98' dh_auto_test - make -j10 check VERBOSE=1 + make -j18 check VERBOSE=1 make[1]: Entering directory '/build/anfo-0.98' Making check in src make[2]: Entering directory '/build/anfo-0.98/src' @@ -5899,7 +5967,7 @@ 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-zZHvBcRn + rm -fr -- /tmp/dh-xdg-rundir-ScQk8bDE create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/anfo.substvars debian/libanfo0.substvars debian/libanfo0-dev.substvars @@ -5913,8 +5981,8 @@ 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/i386-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libanfo.la '/build/anfo-0.98/debian/tmp/usr/lib/i386-linux-gnu' + /usr/bin/mkdir -p '/build/anfo-0.98/debian/tmp/usr/lib/i386-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libanfo.la '/build/anfo-0.98/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libanfo.so.0.0.0 /build/anfo-0.98/debian/tmp/usr/lib/i386-linux-gnu/libanfo.so.0.0.0 libtool: install: (cd /build/anfo-0.98/debian/tmp/usr/lib/i386-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/i386-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; }; }) @@ -5923,8 +5991,8 @@ libtool: install: chmod 644 /build/anfo-0.98/debian/tmp/usr/lib/i386-linux-gnu/libanfo.a libtool: install: ranlib /build/anfo-0.98/debian/tmp/usr/lib/i386-linux-gnu/libanfo.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-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/i386-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/i386-linux-gnu' @@ -5933,19 +6001,19 @@ 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/i386-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/i386-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/i386-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' @@ -5954,15 +6022,15 @@ 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' @@ -6009,8 +6077,8 @@ install -d debian/libanfo0-dev/usr/share/doc/libanfo0-dev install -p -m0644 debian/copyright debian/libanfo0-dev/usr/share/doc/libanfo0-dev/copyright dh_installchangelogs - install -p -m0644 debian/changelog debian/libanfo0/usr/share/doc/libanfo0/changelog.Debian install -p -m0644 debian/changelog debian/anfo/usr/share/doc/anfo/changelog.Debian + install -p -m0644 debian/changelog debian/libanfo0/usr/share/doc/libanfo0/changelog.Debian install -p -m0644 debian/changelog debian/libanfo0-dev/usr/share/doc/libanfo0-dev/changelog.Debian rm -f debian/anfo.debhelper.log debian/libanfo0-dev.debhelper.log debian/libanfo0.debhelper.log debian/rules override_dh_installman @@ -6027,14 +6095,14 @@ chmod 0644 -- debian/anfo/usr/share/man/man1/anfo-tool.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/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 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/file-info.1.dh-new debian/anfo/usr/share/man/man1/file-info.1 - chmod 0644 -- debian/anfo/usr/share/man/man1/file-info.1 - mv debian/anfo/usr/share/man/man1/anfo.1.dh-new debian/anfo/usr/share/man/man1/anfo.1 - chmod 0644 -- debian/anfo/usr/share/man/man1/anfo.1 # delete unused manpage find debian/anfo -name anfo-sge.1 -delete make[1]: Leaving directory '/build/anfo-0.98' @@ -6062,23 +6130,23 @@ debian/rules override_dh_fixperms make[1]: Entering directory '/build/anfo-0.98' dh_fixperms - find debian/libanfo0-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/anfo ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libanfo0 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s + find debian/libanfo0-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libanfo0/usr/share/doc -type f -a -true -a ! -regex 'debian/libanfo0/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libanfo0-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libanfo0-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/anfo/usr/share/doc -type f -a -true -a ! -regex 'debian/anfo/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libanfo0-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/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 -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/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/usr/share/man -type f -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/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libanfo0-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/anfo -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/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/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' @@ -6090,10 +6158,10 @@ dwz -- debian/libanfo0/usr/lib/i386-linux-gnu/libanfo.so.0.0.0 dh_strip -a strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/libanfo0-dev/usr/lib/i386-linux-gnu/libanfo.a - install -d debian/.debhelper/libanfo0/dbgsym-root/usr/lib/debug/.build-id/54 - objcopy --only-keep-debug --compress-debug-sections debian/libanfo0/usr/lib/i386-linux-gnu/libanfo.so.0.0.0 debian/.debhelper/libanfo0/dbgsym-root/usr/lib/debug/.build-id/54/c087322b0b2841b8ac3a7d5c32446e9c4c6670.debug install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/c1 objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/bin/fa2dna debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/c1/a222f5672497cc8789b27e3db6ca79eface056.debug + install -d debian/.debhelper/libanfo0/dbgsym-root/usr/lib/debug/.build-id/54 + objcopy --only-keep-debug --compress-debug-sections debian/libanfo0/usr/lib/i386-linux-gnu/libanfo.so.0.0.0 debian/.debhelper/libanfo0/dbgsym-root/usr/lib/debug/.build-id/54/c087322b0b2841b8ac3a7d5c32446e9c4c6670.debug chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/c1/a222f5672497cc8789b27e3db6ca79eface056.debug strip --remove-section=.comment --remove-section=.note debian/anfo/usr/bin/fa2dna objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/c1/a222f5672497cc8789b27e3db6ca79eface056.debug debian/anfo/usr/bin/fa2dna @@ -6112,16 +6180,16 @@ chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/e7/8b7c53ab370e5754d351264b0434c0da02d11a.debug strip --remove-section=.comment --remove-section=.note debian/anfo/usr/bin/dnaindex objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/e7/8b7c53ab370e5754d351264b0434c0da02d11a.debug debian/anfo/usr/bin/dnaindex - install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/e8 - objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/lib/anfo/index-test debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/e8/2200523829da16c8845b9da09ce9cc3a23afd7.debug - chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/e8/2200523829da16c8845b9da09ce9cc3a23afd7.debug - strip --remove-section=.comment --remove-section=.note debian/anfo/usr/lib/anfo/index-test - objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/e8/2200523829da16c8845b9da09ce9cc3a23afd7.debug debian/anfo/usr/lib/anfo/index-test install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/cb objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/lib/anfo/file-info debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/cb/c5fb668d9d7626df1a6c1180bb2246a47dd923.debug chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/cb/c5fb668d9d7626df1a6c1180bb2246a47dd923.debug strip --remove-section=.comment --remove-section=.note debian/anfo/usr/lib/anfo/file-info objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/cb/c5fb668d9d7626df1a6c1180bb2246a47dd923.debug debian/anfo/usr/lib/anfo/file-info + install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/e8 + objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/lib/anfo/index-test debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/e8/2200523829da16c8845b9da09ce9cc3a23afd7.debug + chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/e8/2200523829da16c8845b9da09ce9cc3a23afd7.debug + strip --remove-section=.comment --remove-section=.note debian/anfo/usr/lib/anfo/index-test + objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/e8/2200523829da16c8845b9da09ce9cc3a23afd7.debug debian/anfo/usr/lib/anfo/index-test install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/anfo/usr/lib/debug/.dwz/i386-linux-gnu debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/anfo/usr/lib/debug/.dwz @@ -6144,7 +6212,7 @@ dh_shlibdeps -a dpkg-shlibdeps -Tdebian/libanfo0.substvars debian/libanfo0/usr/lib/i386-linux-gnu/libanfo.so.0.0.0 install -d debian/anfo/DEBIAN - dpkg-shlibdeps -Tdebian/anfo.substvars debian/anfo/usr/bin/fa2dna debian/anfo/usr/bin/anfo-tool debian/anfo/usr/bin/anfo debian/anfo/usr/bin/dnaindex debian/anfo/usr/lib/anfo/index-test debian/anfo/usr/lib/anfo/file-info + dpkg-shlibdeps -Tdebian/anfo.substvars debian/anfo/usr/bin/fa2dna debian/anfo/usr/bin/anfo-tool debian/anfo/usr/bin/anfo debian/anfo/usr/bin/dnaindex debian/anfo/usr/lib/anfo/file-info debian/anfo/usr/lib/anfo/index-test dh_installdeb install -p -m0644 debian/.debhelper/generated/libanfo0/triggers debian/libanfo0/DEBIAN/triggers install -d debian/libanfo0-dev/DEBIAN @@ -6152,54 +6220,57 @@ echo misc:Depends= >> debian/libanfo0-dev.substvars echo misc:Pre-Depends= >> debian/libanfo0-dev.substvars dpkg-gencontrol -plibanfo0-dev -ldebian/changelog -Tdebian/libanfo0-dev.substvars -Pdebian/libanfo0-dev - echo misc:Depends= >> debian/libanfo0.substvars - echo misc:Pre-Depends= >> debian/libanfo0.substvars - install -d debian/.debhelper/libanfo0/dbgsym-root/DEBIAN - dpkg-gencontrol -plibanfo0 -ldebian/changelog -Tdebian/libanfo0.substvars -Pdebian/.debhelper/libanfo0/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=libanfo0-dbgsym "-DDepends=libanfo0 (= \${binary:Version})" "-DDescription=debug symbols for libanfo0" -DBuild-Ids=54c087322b0b2841b8ac3a7d5c32446e9c4c6670 -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=be148c75c9a6e70b9261518500db3b1c8a370123 c1a222f5672497cc8789b27e3db6ca79eface056 cbc5fb668d9d7626df1a6c1180bb2246a47dd923 e78b7c53ab370e5754d351264b0434c0da02d11a e82200523829da16c8845b9da09ce9cc3a23afd7 f92d8f0917ed681c4e10d2294a8d94c4255a6ef2" -DSection=debug -UMulti-Arch -UReplaces -UBreaks - chmod 0644 -- debian/.debhelper/libanfo0/dbgsym-root/DEBIAN/control - dpkg-gencontrol -plibanfo0 -ldebian/changelog -Tdebian/libanfo0.substvars -Pdebian/libanfo0 + 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=54c087322b0b2841b8ac3a7d5c32446e9c4c6670 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/libanfo0-dev/DEBIAN/control 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/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/anfo >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libanfo0-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libanfo0/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 cd debian/.debhelper/libanfo0/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + chmod 0644 -- debian/anfo/DEBIAN/md5sums chmod 0644 -- debian/libanfo0-dev/DEBIAN/md5sums - chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/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 dh_builddeb - dpkg-deb --root-owner-group --build debian/anfo .. - dpkg-deb --root-owner-group --build debian/.debhelper/anfo/dbgsym-root .. dpkg-deb --root-owner-group --build debian/libanfo0 .. dpkg-deb --root-owner-group --build debian/.debhelper/libanfo0/dbgsym-root .. - dpkg-deb --root-owner-group --build debian/libanfo0-dev .. + dpkg-deb --root-owner-group --build debian/anfo .. dpkg-deb: building package 'libanfo0-dbgsym' in '../libanfo0-dbgsym_0.98-8_i386.deb'. -dpkg-deb: building package 'libanfo0-dev' in '../libanfo0-dev_0.98-8_i386.deb'. -dpkg-deb: building package 'anfo-dbgsym' in '../anfo-dbgsym_0.98-8_i386.deb'. dpkg-deb: building package 'anfo' in '../anfo_0.98-8_i386.deb'. + dpkg-deb --root-owner-group --build debian/libanfo0-dev .. + dpkg-deb --root-owner-group --build debian/.debhelper/anfo/dbgsym-root .. dpkg-deb: building package 'libanfo0' in '../libanfo0_0.98-8_i386.deb'. +dpkg-deb: building package 'libanfo0-dev' in '../libanfo0-dev_0.98-8_i386.deb'. +dpkg-deb: building package 'anfo-dbgsym' in '../anfo-dbgsym_0.98-8_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../anfo_0.98-8_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) +I: copying local configuration +I: user script /srv/workspace/pbuilder/32327/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/32327/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/4051 and its subdirectories -I: Current time: Thu Jun 17 16:29:17 -12 2021 -I: pbuilder-time-stamp: 1623990557 +I: removing directory /srv/workspace/pbuilder/32327 and its subdirectories +I: Current time: Fri Jul 22 00:53:20 +14 2022 +I: pbuilder-time-stamp: 1658400800