I: pbuilder: network access will be disabled during build I: Current time: Mon Sep 12 05:50:03 +14 2022 I: pbuilder-time-stamp: 1662911403 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [hisat2_2.1.0-2.dsc] I: copying [./hisat2_2.1.0.orig.tar.xz] I: copying [./hisat2_2.1.0-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Sep 25 00:07:12 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hisat2_2.1.0-2.dsc dpkg-source: info: extracting hisat2 in hisat2-2.1.0 dpkg-source: info: unpacking hisat2_2.1.0.orig.tar.xz dpkg-source: info: unpacking hisat2_2.1.0-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening dpkg-source: info: applying reproducibile dpkg-source: info: applying fix-freebsd dpkg-source: info: applying compilerflags I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/31597/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/31597/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/31597/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=2868d73318fc48afb69a2d6890ad683c LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=31597 PS4='+ ' 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.MnSeyLHcAx/pbuilderrc_nFME --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.MnSeyLHcAx/b2 --logfile b2/build.log hisat2_2.1.0-2.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-0.bpo.8-amd64 #1 SMP Debian 5.10.46-2~bpo10+1 (2021-07-22) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Sep 12 05:50 sh -> bash lrwxrwxrwx 1 root root 4 Sep 10 04:47 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/31597/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), help2man, pandoc, python dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc is not installed. pbuilder-satisfydepends-dummy depends on python; however: Package python is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} liblocale-gettext-perl{a} liblua5.1-0{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} mime-support{a} pandoc{a} pandoc-data{a} po-debconf{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 54 newly installed, 0 to remove and 0 not upgraded. Need to get 40.5 MB of archives. After unpacking 209 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u6 [1539 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 help2man amd64 1.47.8 [177 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 liblua5.1-0 amd64 5.1.5-8.1+b2 [111 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 pandoc-data all 2.2.1-3 [329 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 pandoc amd64 2.2.1-3+b2 [14.7 MB] Fetched 40.5 MB in 2s (23.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:amd64. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_amd64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_amd64.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_amd64.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u6_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u6) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... 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Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 20658 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_amd64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... 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Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/hisat2-2.1.0/ && 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 hisat2 dpkg-buildpackage: info: source version 2.1.0-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_auto_clean make -j16 clean make[1]: Entering directory '/build/hisat2-2.1.0' rm -f hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l hisat2-build-s-debug hisat2-build-l-debug hisat2-align-s-debug hisat2-align-l-debug hisat2-inspect-s-debug hisat2-inspect-l-debug \ hisat2-build-s.exe hisat2-build-l.exe hisat2-align-s.exe hisat2-align-l.exe hisat2-inspect-s.exe hisat2-inspect-l.exe hisat2-build-s-debug.exe hisat2-build-l-debug.exe hisat2-align-s-debug.exe hisat2-align-l-debug.exe hisat2-inspect-s-debug.exe hisat2-inspect-l-debug.exe \ hisat2-src.zip hisat2-bin.zip rm -f core.* .tmp.head rm -rf *.dSYM make[1]: Leaving directory '/build/hisat2-2.1.0' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/hisat2-2.1.0' make BUILD_HOST='Debian' \ BUILD_TIME="24 September 2018" \ all doc make[2]: Entering directory '/build/hisat2-2.1.0' /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"24 September 2018\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/hisat2-2.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^~~~~~~~~~~~~~ /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"24 September 2018\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/hisat2-2.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -o hisat2-build-l hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^~~~~~~~~~~~~~ /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"24 September 2018\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/hisat2-2.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -o hisat2-align-s hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1753:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr presets(new PresetsV0()); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3068:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp:3069:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ps(patsrcFact->create()); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp:3085:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’: hisat2.cpp:3826:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr refs( ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]’: hisat2.cpp:3686:17: required from ‘void driver(const char*, const string&, const string&) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]’ hisat2.cpp:4115:51: required from here gfm.h:6451:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] int lastorig = -1; ^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1542:4: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:5003:9: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:1172:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(new_node_bot - new_node_top < gws.map.size()) { group_walk.h:1183:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(index_t j = 0; j + 1 < gws.map.size(); j++) { group_walk.h:1238:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(node_range.second - node_range.first < st.back().map_.size()) { group_walk.h:1249:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2625:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(rfoff >= contig_len) return 0; ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2703:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(alt_range.first >= alts.size()) { hi_aligner.h:2868:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] for(int i = 0; i < alt.len; i++) { ~~^~~~~~~~~ hi_aligner.h:2909:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { ~~~~~^~~~~~~~ hi_aligner.h:2985:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] if(alignedLen == next_rdlen) return rdlen; ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3021:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] if(mm_max_rd_i + rdoff > best_rdoff) { ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3026:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] } else if(mm_max_rd_i + rdoff == best_rdoff) { ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3278:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] if(best_rdoff < rdoff + rd_i) { ~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:492:66: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ group_walk.h:1478:3: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:4998:5: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:794:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(new_top - top < tmp_gbwt_to_node.size()) { group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(new_top - top == tmp_gbwt_to_node.size()) { group_walk.h:817:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(i + 1 < tmp_zOffs.size()) { group_walk.h:823:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(new_bot2 - top < tmp_gbwt_to_node.size()) { group_walk.h:830:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(new_bot2 - top < tmp_gbwt_to_node.size()) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = unsigned int]’: hi_aligner.h:2739:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2484:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(ht_range.first >= haplotypes.size()) hi_aligner.h:2499:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] if(ht_list[h].first == ht_range.first) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2537:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] if(ht_list[h].first == ht_range.first) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2561:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(; ht_range.second < haplotypes.size(); ht_range.second++) { hi_aligner.h:2568:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] if(ht_list[h].first == ht_range.second) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from hisat2.cpp:45: spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:214:9: required from here spliced_aligner.h:282:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] bool another_spliced = false; ^~~~~~~~~~~~~~~ In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘bool GenomeHit::combineWith(const GenomeHit&, const Read&, const GFM&, const BitPairReference&, const ALTDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = unsigned int; TAlScore = long int]’: spliced_aligner.h:365:30: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]’ spliced_aligner.h:214:9: required from here hi_aligner.h:1790:32: warning: comparison of integer expressions of different signedness: ‘const uint64_t’ {aka ‘const long unsigned int’} and ‘char’ [-Wsign-compare] if(alt.seq == rdc) { ~~~~~~~~^~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from aln_sink.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from aln_sink.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ?: using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29, from splice_site.cpp:20: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:59: required from here ds.h:663:14: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] std::memcpy(list_ + cur_, l, bytes); ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from edit.h:30, from splice_site.cpp:20: splice_site.h:377:7: note: ‘class Exon’ declared here class Exon { ^~~~ /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"24 September 2018\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/hisat2-2.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -o hisat2-align-l hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1753:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr presets(new PresetsV0()); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3068:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp:3069:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ps(patsrcFact->create()); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp:3085:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’: hisat2.cpp:3826:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr refs( ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = long unsigned int]’: hisat2.cpp:3686:17: required from ‘void driver(const char*, const string&, const string&) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]’ hisat2.cpp:4115:51: required from here gfm.h:6451:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] int lastorig = -1; ^~~~~~~~ In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’: hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2125:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); ~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1542:4: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:5003:9: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:1172:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(new_node_bot - new_node_top < gws.map.size()) { group_walk.h:1183:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(index_t j = 0; j + 1 < gws.map.size(); j++) { group_walk.h:1238:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(node_range.second - node_range.first < st.back().map_.size()) { group_walk.h:1249:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2625:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(rfoff >= contig_len) return 0; ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2703:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(alt_range.first >= alts.size()) { hi_aligner.h:2868:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] for(int i = 0; i < alt.len; i++) { ~~^~~~~~~~~ hi_aligner.h:2909:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { ~~~~~^~~~~~~~ hi_aligner.h:2985:31: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] if(alignedLen == next_rdlen) return rdlen; ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3021:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] if(mm_max_rd_i + rdoff > best_rdoff) { ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3026:39: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] } else if(mm_max_rd_i + rdoff == best_rdoff) { ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3278:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] if(best_rdoff < rdoff + rd_i) { ~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:492:66: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ group_walk.h:1478:3: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:4998:5: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:794:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(new_top - top < tmp_gbwt_to_node.size()) { group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(new_top - top == tmp_gbwt_to_node.size()) { group_walk.h:817:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(i + 1 < tmp_zOffs.size()) { group_walk.h:823:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] while(new_bot2 - top < tmp_gbwt_to_node.size()) { group_walk.h:830:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(new_bot2 - top < tmp_gbwt_to_node.size()) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = long unsigned int]’: hi_aligner.h:2739:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2484:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(ht_range.first >= haplotypes.size()) hi_aligner.h:2499:37: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] if(ht_list[h].first == ht_range.first) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2537:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] if(ht_list[h].first == ht_range.first) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2561:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(; ht_range.second < haplotypes.size(); ht_range.second++) { hi_aligner.h:2568:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] if(ht_list[h].first == ht_range.second) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from hisat2.cpp:45: spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:214:9: required from here spliced_aligner.h:282:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] bool another_spliced = false; ^~~~~~~~~~~~~~~ spliced_aligner.h:642:65: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) { spliced_aligner.h:1298:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘bool GenomeHit::combineWith(const GenomeHit&, const Read&, const GFM&, const BitPairReference&, const ALTDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = long unsigned int; TAlScore = long int]’: spliced_aligner.h:365:30: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’ spliced_aligner.h:214:9: required from here hi_aligner.h:1790:32: warning: comparison of integer expressions of different signedness: ‘const uint64_t’ {aka ‘const long unsigned int’} and ‘char’ [-Wsign-compare] if(alt.seq == rdc) { ~~~~~~~~^~~~~~ hi_aligner.h: In instantiation of ‘index_t HI_Aligner::globalGFMSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList >&, RandomSource&, bool&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’: spliced_aligner.h:936:25: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’ spliced_aligner.h:214:9: required from here hi_aligner.h:5792:85: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from aln_sink.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from aln_sink.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ?: using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29, from splice_site.cpp:20: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:59: required from here ds.h:663:14: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] std::memcpy(list_ + cur_, l, bytes); ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from edit.h:30, from splice_site.cpp:20: splice_site.h:377:7: note: ‘class Exon’ declared here class Exon { ^~~~ /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"24 September 2018\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/hisat2-2.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \ -I third_party -I . \ -o hisat2-inspect-s hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] if(!((a) <= (b))) { \ ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ assert_leq(fw, 1); ^~~~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] if(!((a) <= (b))) { \ ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ assert_leq(fw, 1); ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] if(!((a) <= (b))) { \ ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ assert_leq(fw, 1); ^~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"24 September 2018\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/hisat2-2.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \ -I third_party -I . \ -o hisat2-inspect-l hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] if(!((a) <= (b))) { \ ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ assert_leq(fw, 1); ^~~~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] if(!((a) <= (b))) { \ ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ assert_leq(fw, 1); ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/bits/locale_conv.h:41, from /usr/include/c++/8/locale:43, from /usr/include/c++/8/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] if(!((a) <= (b))) { \ ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ assert_leq(fw, 1); ^~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/8/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ make[2]: Nothing to be done for 'doc'. make[2]: Leaving directory '/build/hisat2-2.1.0' help2man ./hisat2 --no-info --name \ 'graph-based alignment of short nucleotide reads to many genomes, wrapper script' \ > debian/hisat2.1 help2man ./hisat2-align-l --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, large index binary' \ --no-info > debian/hisat2-align-l.1 help2man ./hisat2-align-s --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, small index binary' \ --no-info > debian/hisat2-align-s.1 help2man ./hisat2-build --name 'HISAT2 indexer, wrapper script' \ --no-info > debian/hisat2-build.1 #rm hisat2-buildc help2man ./hisat2-build-l --name 'HISAT2 indexer, large index binary' \ --no-info > debian/hisat2-build-l.1 help2man ./hisat2-build-s --name 'HISAT2 indexer, small index binary' \ --no-info > debian/hisat2-build-s.1 help2man ./hisat2-inspect --name 'HISAT2 index inspector, wrapper script' \ --no-info > debian/hisat2-inspect.1 help2man ./hisat2-inspect-l --name 'HISAT2 index inspector, large index binary' \ --no-info > debian/hisat2-inspect-l.1 help2man ./hisat2-inspect-s --name 'HISAT2 index inspector, small index binary' \ --no-info > debian/hisat2-inspect-s.1 make[1]: Leaving directory '/build/hisat2-2.1.0' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/hisat2-2.1.0' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/hisat2-2.1.0' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'hisat2-dbgsym' in '../hisat2-dbgsym_2.1.0-2_amd64.deb'. dpkg-deb: building package 'hisat2' in '../hisat2_2.1.0-2_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../hisat2_2.1.0-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/31597/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/31597/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/31597 and its subdirectories I: Current time: Mon Sep 12 06:00:15 +14 2022 I: pbuilder-time-stamp: 1662912015