I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 27 23:45:50 +14 2021 I: pbuilder-time-stamp: 1630057550 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 [bowtie_1.2.2+dfsg-4.dsc] I: copying [./bowtie_1.2.2+dfsg.orig.tar.xz] I: copying [./bowtie_1.2.2+dfsg-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Sep 6 04:53:14 2018 +14 gpgv: using RSA key B1A51EB2779DD01743CC19BA1CF792111B5228B0 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bowtie_1.2.2+dfsg-4.dsc dpkg-source: info: extracting bowtie in bowtie-1.2.2+dfsg dpkg-source: info: unpacking bowtie_1.2.2+dfsg.orig.tar.xz dpkg-source: info: unpacking bowtie_1.2.2+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_isa_return.patch dpkg-source: info: applying no_hash_style_both_for_mips.patch dpkg-source: info: applying use-dpkg-buildflags.patch dpkg-source: info: applying use_debian_seqan.patch dpkg-source: info: applying seqan-fix-setBegin-call.patch dpkg-source: info: applying seqan-rename-ChunkPool.patch dpkg-source: info: applying seqan-rename-fill-to-resize.patch dpkg-source: info: applying disable_bits_flag.patch dpkg-source: info: applying seqan-popcount.patch dpkg-source: info: applying bowtie_ContextLss-1.1-1.4.patch dpkg-source: info: applying ppc64el.patch dpkg-source: info: applying enable_arm64.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying gcc-64bit.patch dpkg-source: info: applying build-as-Cpp03.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/5915/tmp/hooks/D01_modify_environment starting debug: Running on codethink-sled9-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/5915/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/5915/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]="aarch64-unknown-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=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=5915 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.BtiDkpqQ1k/pbuilderrc_Opt1 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.BtiDkpqQ1k/b2 --logfile b2/build.log bowtie_1.2.2+dfsg-4.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 18 2019 bash -rwxr-xr-x 3 root root 34808 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 34808 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 34808 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14264 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 35576 Mar 1 2019 cat -rwxr-xr-x 1 root root 60256 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 56096 Mar 1 2019 chmod -rwxr-xr-x 1 root root 64368 Mar 1 2019 chown -rwxr-xr-x 1 root root 134632 Mar 1 2019 cp -rwxr-xr-x 1 root root 129536 Jan 18 2019 dash -rwxr-xr-x 1 root root 97136 Mar 1 2019 date -rwxr-xr-x 1 root root 76736 Mar 1 2019 dd -rwxr-xr-x 1 root root 93752 Mar 1 2019 df -rwxr-xr-x 1 root root 138848 Mar 1 2019 dir -rwxr-xr-x 1 root root 75984 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 31368 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 27256 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 174304 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 89656 Jan 6 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 27 2018 hostname -rwxr-xr-x 1 root root 64472 Mar 1 2019 ln -rwxr-xr-x 1 root root 52544 Jul 27 2018 login -rwxr-xr-x 1 root root 138848 Mar 1 2019 ls -rwxr-xr-x 1 root root 108552 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 76840 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 64480 Mar 1 2019 mknod -rwxr-xr-x 1 root root 39736 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 10 2019 more -rwsr-xr-x 1 root root 47112 Jan 10 2019 mount -rwxr-xr-x 1 root root 14344 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138736 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 35560 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68440 Mar 1 2019 rm -rwxr-xr-x 1 root root 39624 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Aug 27 23:46 sh -> bash lrwxrwxrwx 1 root root 4 Aug 27 04:51 sh.distrib -> dash -rwxr-xr-x 1 root root 31384 Mar 1 2019 sleep -rwxr-xr-x 1 root root 72480 Mar 1 2019 stty -rwsr-xr-x 1 root root 59424 Jan 10 2019 su -rwxr-xr-x 1 root root 31416 Mar 1 2019 sync -rwxr-xr-x 1 root root 449416 Apr 24 2019 tar -rwxr-xr-x 1 root root 10560 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 88968 Mar 1 2019 touch -rwxr-xr-x 1 root root 27256 Mar 1 2019 true -rwxr-xr-x 1 root root 14264 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 10 2019 umount -rwxr-xr-x 1 root root 31384 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138848 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34824 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/5915/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: arm64 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, libtbb-dev, python, seqan-dev (>= 1.4), zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 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 libtbb-dev; however: Package libtbb-dev is not installed. pbuilder-satisfydepends-dummy depends on python; however: Package python is not installed. pbuilder-satisfydepends-dummy depends on seqan-dev (>= 1.4); however: Package seqan-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev 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} 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} libtbb-dev{a} libtbb2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{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} seqan-dev{a} zlib1g-dev{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 26.3 MB of archives. After unpacking 105 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 libpython2.7-minimal arm64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 python2.7-minimal arm64 2.7.16-2+deb10u1 [1292 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 python2-minimal arm64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 python-minimal arm64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libexpat1 arm64 2.2.6-2+deb10u1 [85.4 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libpython2.7-stdlib arm64 2.7.16-2+deb10u1 [1890 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 python2.7 arm64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libpython2-stdlib arm64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libpython-stdlib arm64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 python2 arm64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 python arm64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 liblocale-gettext-perl arm64 1.07-3+b4 [18.8 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 help2man arm64 1.47.8 [177 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 libtbb2 arm64 2018~U6-4 [122 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 libtbb-dev arm64 2018~U6-4 [286 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 seqan-dev all 1.4.2+dfsg-3 [1096 kB] Get: 54 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] Fetched 26.3 MB in 1s (19.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:arm64. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_arm64.deb ... Unpacking libpython2.7-minimal:arm64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_arm64.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_arm64.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_arm64.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:arm64. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u3_arm64.deb ... Unpacking libssl1.1:arm64 (1.1.1d-0+deb10u3) ... 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:arm64. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_arm64.deb ... Unpacking libexpat1:arm64 (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) ... Selecting previously unselected package libreadline7:arm64. 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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/bowtie-1.2.2+dfsg/ && 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 bowtie dpkg-buildpackage: info: source version 1.2.2+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Mestiashvili dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/bowtie-1.2.2+dfsg' rm -f .bowtie* dh_auto_clean make -j8 clean make[2]: Entering directory '/build/bowtie-1.2.2+dfsg' rm -f bowtie-build-s bowtie-build-l bowtie-align-s bowtie-align-l bowtie-inspect-s bowtie-inspect-l bowtie-build-s-debug bowtie-build-l-debug bowtie-align-s-debug bowtie-align-l-debug bowtie-inspect-s-debug bowtie-inspect-l-debug \ bowtie_prof \ bowtie-build-s.exe bowtie-build-l.exe bowtie-align-s.exe bowtie-align-l.exe bowtie-inspect-s.exe bowtie-inspect-l.exe bowtie-build-s-debug.exe bowtie-build-l-debug.exe bowtie-align-s-debug.exe bowtie-align-l-debug.exe bowtie-inspect-s-debug.exe bowtie-inspect-l-debug.exe bowtie_prof.exe \ bowtie-src.zip bowtie-bin.zip rm -f core.* rm -f bowtie-align-s-master* bowtie-align-s-no-io* rm -rf .lib .include make[2]: Leaving directory '/build/bowtie-1.2.2+dfsg' make[1]: Leaving directory '/build/bowtie-1.2.2+dfsg' 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/bowtie-1.2.2+dfsg' /usr/bin/make allall make[2]: Entering directory '/build/bowtie-1.2.2+dfsg' g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now\"" -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \ -isystem /usr/include/seqan \ -o bowtie-build-s ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bowtie_build_main.cpp \ -Wl,-z,relro -Wl,-z,now -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:19, from ebwt.h:27, from ebwt_build.cpp:11: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:162:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:163:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from ebwt.h:27, from ebwt_build.cpp:11: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:204:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:204:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ In file included from ebwt.h:31, from ebwt_build.cpp:11: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from ebwt.h:39, from ebwt_build.cpp:11: reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ In file included from ebwt_build.cpp:11: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:826:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:827:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:834:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:835:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from ebwt.h:27, from ebwt_build.cpp:11: blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = seqan::String, seqan::Alloc<> >; TIndexOffU = unsigned int]': blockwise_sa.h:287:23: required from here blockwise_sa.h:297:26: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < length(_sampleSuffs) + 1; i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = seqan::String, seqan::Packed<> >; TIndexOffU = unsigned int]': blockwise_sa.h:287:23: required from here blockwise_sa.h:297:26: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] alphabet.cpp:293:1: warning: narrowing conversion of '-1' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] }; ^ g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now\"" -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \ -isystem /usr/include/seqan \ -o bowtie-build-l ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bowtie_build_main.cpp \ -Wl,-z,relro -Wl,-z,now -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:19, from ebwt.h:27, from ebwt_build.cpp:11: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:162:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:163:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from ebwt.h:27, from ebwt_build.cpp:11: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:204:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:204:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ In file included from ebwt.h:31, from ebwt_build.cpp:11: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from ebwt.h:39, from ebwt_build.cpp:11: reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ In file included from ebwt_build.cpp:11: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:826:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:827:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:834:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:835:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from ebwt.h:27, from ebwt_build.cpp:11: blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = seqan::String, seqan::Alloc<> >; TIndexOffU = long unsigned int]': blockwise_sa.h:287:23: required from here blockwise_sa.h:297:26: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < length(_sampleSuffs) + 1; i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = seqan::String, seqan::Packed<> >; TIndexOffU = long unsigned int]': blockwise_sa.h:287:23: required from here blockwise_sa.h:297:26: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] alphabet.cpp:293:1: warning: narrowing conversion of '-1' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] }; ^ g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now\"" -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \ -isystem /usr/include/seqan \ -o bowtie-align-s ebwt_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \ -Wl,-z,relro -Wl,-z,now -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:19, from ebwt.h:27, from ebwt_search.cpp:21: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:162:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:163:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from ebwt.h:27, from ebwt_search.cpp:21: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:204:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:204:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ In file included from ebwt.h:31, from ebwt_search.cpp:21: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from ebwt.h:39, from ebwt_search.cpp:21: reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ In file included from ebwt_search.cpp:21: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:826:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:827:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:834:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:835:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ alphabet.cpp:293:1: warning: narrowing conversion of '-1' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] }; ^ pat.cpp: In member function 'std::pair PatternSourcePerThread::nextReadPair()': pat.cpp:109:36: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] bool this_is_last = buf_.cur_buf_ == last_batch_size_-1; ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ pat.cpp: In member function 'virtual bool FastaPatternSource::parse(Read&, Read&, TReadId) const': pat.cpp:711:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for(size_t i = 0; i < seqoff - trim3; i++) { ~~^~~~~~~~~~~~~~~~ pat.cpp: In member function 'virtual bool FastaContinuousPatternSource::parse(Read&, Read&, TReadId) const': pat.cpp:888:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for(size_t i = 0; i < seqoff; i++) { ~~^~~~~~~~ In file included from ebwt_search_util.h:9, from ebwt_search_util.cpp:1: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from sam.cpp:12: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from hit.cpp:1: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now\"" -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -DBOWTIE_64BIT_INDEX -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \ -isystem /usr/include/seqan \ -o bowtie-align-l ebwt_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \ -Wl,-z,relro -Wl,-z,now -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:19, from ebwt.h:27, from ebwt_search.cpp:21: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:162:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:163:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from ebwt.h:27, from ebwt_search.cpp:21: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:204:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:204:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ In file included from ebwt.h:31, from ebwt_search.cpp:21: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from ebwt.h:39, from ebwt_search.cpp:21: reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ In file included from ebwt_search.cpp:21: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:826:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:827:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:834:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:835:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ alphabet.cpp:293:1: warning: narrowing conversion of '-1' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] }; ^ pat.cpp: In member function 'std::pair PatternSourcePerThread::nextReadPair()': pat.cpp:109:36: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] bool this_is_last = buf_.cur_buf_ == last_batch_size_-1; ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ pat.cpp: In member function 'virtual bool FastaPatternSource::parse(Read&, Read&, TReadId) const': pat.cpp:711:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for(size_t i = 0; i < seqoff - trim3; i++) { ~~^~~~~~~~~~~~~~~~ pat.cpp: In member function 'virtual bool FastaContinuousPatternSource::parse(Read&, Read&, TReadId) const': pat.cpp:888:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for(size_t i = 0; i < seqoff; i++) { ~~^~~~~~~~ In file included from ebwt_search_util.h:9, from ebwt_search_util.cpp:1: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from sam.cpp:12: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from hit.cpp:1: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { g++ -O3 \ -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now\"" -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \ -isystem /usr/include/seqan -I . \ -o bowtie-inspect-s bowtie_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp \ -Wl,-z,relro -Wl,-z,now -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:162:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:163:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from ebwt.h:27, from bowtie_inspect.cpp:10: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:204:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:204:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ In file included from ebwt.h:31, from bowtie_inspect.cpp:10: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from bowtie_inspect.cpp:10: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:826:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:827:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:834:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:835:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::free(T*, uint32_t) [with T = Edit; uint32_t = unsigned int]': range_source.h:138:75: required from here pool.h:306:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, num * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'void AllocOnlyPool::free(T*) [with T = Branch]': range_source.h:789:18: required from here pool.h:286:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from bowtie_inspect.cpp:10: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Edit]': pool.h:238:7: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Edit]': pool.h:240:8: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Branch]': pool.h:215:7: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from bowtie_inspect.cpp:10: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Branch]': pool.h:217:8: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from bowtie_inspect.cpp:10: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ alphabet.cpp:293:1: warning: narrowing conversion of '-1' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] }; ^ g++ -O3 \ -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now\"" -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \ -isystem /usr/include/seqan -I . \ -o bowtie-inspect-l bowtie_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp \ -Wl,-z,relro -Wl,-z,now -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:162:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:163:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from ebwt.h:27, from bowtie_inspect.cpp:10: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:204:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:204:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ In file included from ebwt.h:31, from bowtie_inspect.cpp:10: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from bowtie_inspect.cpp:10: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:826:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:827:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:834:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:835:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::free(T*, uint32_t) [with T = Edit; uint32_t = unsigned int]': range_source.h:138:75: required from here pool.h:306:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, num * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'void AllocOnlyPool::free(T*) [with T = Branch]': range_source.h:789:18: required from here pool.h:286:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from bowtie_inspect.cpp:10: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Edit]': pool.h:238:7: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Edit]': pool.h:240:8: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Branch]': pool.h:215:7: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from bowtie_inspect.cpp:10: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Branch]': pool.h:217:8: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from bowtie_inspect.cpp:10: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ alphabet.cpp:293:1: warning: narrowing conversion of '-1' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] }; ^ g++ -O0 -g3 -DCOMPILER_OPTIONS="\"-O0 -g3 -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now\"" -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \ -isystem /usr/include/seqan \ -o bowtie-build-s-debug ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bowtie_build_main.cpp \ -Wl,-z,relro -Wl,-z,now -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:19, from ebwt.h:27, from ebwt_build.cpp:11: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:162:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:163:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from ebwt.h:27, from ebwt_build.cpp:11: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:204:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:204:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ In file included from ebwt.h:31, from ebwt_build.cpp:11: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from ebwt_build.cpp:11: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:826:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:827:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:834:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:835:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from ebwt_build.cpp:9: pool.h: In instantiation of 'bool AllocOnlyPool::free(T*, uint32_t) [with T = Edit; uint32_t = unsigned int]': range_source.h:138:75: required from here pool.h:306:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, num * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from ebwt_build.cpp:11: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from ebwt_build.cpp:9: pool.h: In instantiation of 'void AllocOnlyPool::free(T*) [with T = Branch]': range_source.h:789:18: required from here pool.h:286:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from ebwt_build.cpp:11: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from ebwt_build.cpp:9: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Edit]': pool.h:238:7: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from ebwt_build.cpp:11: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from ebwt_build.cpp:9: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Edit]': pool.h:240:8: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from ebwt_build.cpp:11: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from ebwt_build.cpp:9: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Branch]': pool.h:215:7: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from ebwt_build.cpp:11: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from ebwt_build.cpp:9: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Branch]': pool.h:217:8: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from ebwt_build.cpp:11: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from ebwt.h:27, from ebwt_build.cpp:11: blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = seqan::String, seqan::Alloc<> >; TIndexOffU = unsigned int]': blockwise_sa.h:287:23: required from here blockwise_sa.h:297:26: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < length(_sampleSuffs) + 1; i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ebwt_build.cpp:9: blockwise_sa.h: In instantiation of 'void KarkkainenBlockwiseSA::nextBlock(int, int) [with TStr = seqan::String, seqan::Alloc<> >]': blockwise_sa.h:970:6: required from here assert_helpers.h:176:9: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!(a < b)) { \ ~~~^~~~ blockwise_sa.h:973:3: note: in expansion of macro 'assert_lt' assert_lt(tid, length(this->_itrBuckets)); ^~~~~~~~~ assert_helpers.h:207:11: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!((a) <= (b))) { \ ~~~~~^~~~~~~ assert_helpers.h:207:11: note: in definition of macro 'assert_leq' if(!((a) <= (b))) { \ ^~ assert_helpers.h:176:9: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!(a < b)) { \ ~~~^~~~ blockwise_sa.h:1054:5: note: in expansion of macro 'assert_lt' assert_lt(cur_block, length(_sampleSuffs)); ^~~~~~~~~ assert_helpers.h:207:11: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!((a) <= (b))) { \ ~~~~~^~~~~~~ assert_helpers.h:207:11: note: in definition of macro 'assert_leq' if(!((a) <= (b))) { \ ^~ In file included from ebwt.h:27, from ebwt_build.cpp:11: blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = seqan::String, seqan::Packed<> >; TIndexOffU = unsigned int]': blockwise_sa.h:287:23: required from here blockwise_sa.h:297:26: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < length(_sampleSuffs) + 1; i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ebwt_build.cpp:9: blockwise_sa.h: In instantiation of 'void KarkkainenBlockwiseSA::nextBlock(int, int) [with TStr = seqan::String, seqan::Packed<> >]': blockwise_sa.h:358:16: required from here assert_helpers.h:176:9: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!(a < b)) { \ ~~~^~~~ blockwise_sa.h:973:3: note: in expansion of macro 'assert_lt' assert_lt(tid, length(this->_itrBuckets)); ^~~~~~~~~ assert_helpers.h:207:11: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!((a) <= (b))) { \ ~~~~~^~~~~~~ assert_helpers.h:207:11: note: in definition of macro 'assert_leq' if(!((a) <= (b))) { \ ^~ assert_helpers.h:176:9: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!(a < b)) { \ ~~~^~~~ blockwise_sa.h:1054:5: note: in expansion of macro 'assert_lt' assert_lt(cur_block, length(_sampleSuffs)); ^~~~~~~~~ assert_helpers.h:207:11: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!((a) <= (b))) { \ ~~~~~^~~~~~~ assert_helpers.h:207:11: note: in definition of macro 'assert_leq' if(!((a) <= (b))) { \ ^~ alphabet.cpp:293:1: warning: narrowing conversion of '-1' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] }; ^ g++ -O0 -g3 -DCOMPILER_OPTIONS="\"-O0 -g3 -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now\"" -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \ -isystem /usr/include/seqan \ -o bowtie-build-l-debug ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bowtie_build_main.cpp \ -Wl,-z,relro -Wl,-z,now -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:19, from ebwt.h:27, from ebwt_build.cpp:11: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:162:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:163:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from ebwt.h:27, from ebwt_build.cpp:11: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:204:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:204:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ In file included from ebwt.h:31, from ebwt_build.cpp:11: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from ebwt_build.cpp:11: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:826:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:827:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:834:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:835:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from ebwt_build.cpp:9: pool.h: In instantiation of 'bool AllocOnlyPool::free(T*, uint32_t) [with T = Edit; uint32_t = unsigned int]': range_source.h:138:75: required from here pool.h:306:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, num * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from ebwt_build.cpp:11: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from ebwt_build.cpp:9: pool.h: In instantiation of 'void AllocOnlyPool::free(T*) [with T = Branch]': range_source.h:789:18: required from here pool.h:286:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from ebwt_build.cpp:11: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from ebwt_build.cpp:9: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Edit]': pool.h:238:7: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from ebwt_build.cpp:11: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from ebwt_build.cpp:9: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Edit]': pool.h:240:8: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from ebwt_build.cpp:11: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from ebwt_build.cpp:9: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Branch]': pool.h:215:7: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from ebwt_build.cpp:11: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from ebwt_build.cpp:9: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Branch]': pool.h:217:8: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from ebwt_build.cpp:11: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from ebwt.h:27, from ebwt_build.cpp:11: blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = seqan::String, seqan::Alloc<> >; TIndexOffU = long unsigned int]': blockwise_sa.h:287:23: required from here blockwise_sa.h:297:26: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < length(_sampleSuffs) + 1; i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ebwt_build.cpp:9: blockwise_sa.h: In instantiation of 'void KarkkainenBlockwiseSA::nextBlock(int, int) [with TStr = seqan::String, seqan::Alloc<> >]': blockwise_sa.h:970:6: required from here assert_helpers.h:176:9: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!(a < b)) { \ ~~~^~~~ blockwise_sa.h:973:3: note: in expansion of macro 'assert_lt' assert_lt(tid, length(this->_itrBuckets)); ^~~~~~~~~ assert_helpers.h:207:11: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!((a) <= (b))) { \ ~~~~~^~~~~~~ assert_helpers.h:207:11: note: in definition of macro 'assert_leq' if(!((a) <= (b))) { \ ^~ assert_helpers.h:176:9: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!(a < b)) { \ ~~~^~~~ blockwise_sa.h:1054:5: note: in expansion of macro 'assert_lt' assert_lt(cur_block, length(_sampleSuffs)); ^~~~~~~~~ assert_helpers.h:207:11: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!((a) <= (b))) { \ ~~~~~^~~~~~~ assert_helpers.h:207:11: note: in definition of macro 'assert_leq' if(!((a) <= (b))) { \ ^~ In file included from ebwt.h:27, from ebwt_build.cpp:11: blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = seqan::String, seqan::Packed<> >; TIndexOffU = long unsigned int]': blockwise_sa.h:287:23: required from here blockwise_sa.h:297:26: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < length(_sampleSuffs) + 1; i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ebwt_build.cpp:9: blockwise_sa.h: In instantiation of 'void KarkkainenBlockwiseSA::nextBlock(int, int) [with TStr = seqan::String, seqan::Packed<> >]': blockwise_sa.h:358:16: required from here assert_helpers.h:176:9: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!(a < b)) { \ ~~~^~~~ blockwise_sa.h:973:3: note: in expansion of macro 'assert_lt' assert_lt(tid, length(this->_itrBuckets)); ^~~~~~~~~ assert_helpers.h:207:11: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!((a) <= (b))) { \ ~~~~~^~~~~~~ assert_helpers.h:207:11: note: in definition of macro 'assert_leq' if(!((a) <= (b))) { \ ^~ assert_helpers.h:176:9: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!(a < b)) { \ ~~~^~~~ blockwise_sa.h:1054:5: note: in expansion of macro 'assert_lt' assert_lt(cur_block, length(_sampleSuffs)); ^~~~~~~~~ assert_helpers.h:207:11: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if(!((a) <= (b))) { \ ~~~~~^~~~~~~ assert_helpers.h:207:11: note: in definition of macro 'assert_leq' if(!((a) <= (b))) { \ ^~ alphabet.cpp:293:1: warning: narrowing conversion of '-1' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] }; ^ g++ -O0 -g3 \ -DCOMPILER_OPTIONS="\"-O0 -g3 -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now\"" -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \ -isystem /usr/include/seqan \ -o bowtie-align-s-debug ebwt_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \ -Wl,-z,relro -Wl,-z,now -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:19, from ebwt.h:27, from ebwt_search.cpp:21: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:162:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:163:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from ebwt.h:27, from ebwt_search.cpp:21: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:204:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:204:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ In file included from ebwt.h:31, from ebwt_search.cpp:21: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from ebwt_search.cpp:21: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:826:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:827:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:834:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:835:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from alphabet.h:9, from ebwt_search.cpp:18: pool.h: In instantiation of 'bool AllocOnlyPool::free(T*, uint32_t) [with T = Edit; uint32_t = unsigned int]': range_source.h:138:75: required from here pool.h:306:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, num * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from ebwt_search.cpp:21: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from alphabet.h:9, from ebwt_search.cpp:18: pool.h: In instantiation of 'void AllocOnlyPool::free(T*) [with T = Branch]': range_source.h:789:18: required from here pool.h:286:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from ebwt_search.cpp:21: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from alphabet.h:9, from ebwt_search.cpp:18: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Edit]': pool.h:238:7: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from ebwt_search.cpp:21: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from alphabet.h:9, from ebwt_search.cpp:18: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Edit]': pool.h:240:8: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from ebwt_search.cpp:21: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from alphabet.h:9, from ebwt_search.cpp:18: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Branch]': pool.h:215:7: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from ebwt_search.cpp:21: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from alphabet.h:9, from ebwt_search.cpp:18: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Branch]': pool.h:217:8: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from ebwt_search.cpp:21: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ alphabet.cpp:293:1: warning: narrowing conversion of '-1' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] }; ^ pat.cpp: In member function 'std::pair PatternSourcePerThread::nextReadPair()': pat.cpp:109:36: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] bool this_is_last = buf_.cur_buf_ == last_batch_size_-1; ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ pat.cpp: In member function 'virtual bool FastaPatternSource::parse(Read&, Read&, TReadId) const': pat.cpp:711:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for(size_t i = 0; i < seqoff - trim3; i++) { ~~^~~~~~~~~~~~~~~~ pat.cpp: In member function 'virtual bool FastaContinuousPatternSource::parse(Read&, Read&, TReadId) const': pat.cpp:888:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for(size_t i = 0; i < seqoff; i++) { ~~^~~~~~~~ In file included from ebwt_search_util.h:9, from ebwt_search_util.cpp:1: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from sam.cpp:12: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from hit.cpp:1: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { g++ -O0 -g3 \ -DCOMPILER_OPTIONS="\"-O0 -g3 -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now\"" -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \ -isystem /usr/include/seqan \ -o bowtie-align-l-debug ebwt_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \ -Wl,-z,relro -Wl,-z,now -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:19, from ebwt.h:27, from ebwt_search.cpp:21: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:162:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:163:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from ebwt.h:27, from ebwt_search.cpp:21: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:204:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:204:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ In file included from ebwt.h:31, from ebwt_search.cpp:21: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from ebwt_search.cpp:21: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:826:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:827:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:834:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:835:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from alphabet.h:9, from ebwt_search.cpp:18: pool.h: In instantiation of 'bool AllocOnlyPool::free(T*, uint32_t) [with T = Edit; uint32_t = unsigned int]': range_source.h:138:75: required from here pool.h:306:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, num * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from ebwt_search.cpp:21: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from alphabet.h:9, from ebwt_search.cpp:18: pool.h: In instantiation of 'void AllocOnlyPool::free(T*) [with T = Branch]': range_source.h:789:18: required from here pool.h:286:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from ebwt_search.cpp:21: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from alphabet.h:9, from ebwt_search.cpp:18: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Edit]': pool.h:238:7: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from ebwt_search.cpp:21: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from alphabet.h:9, from ebwt_search.cpp:18: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Edit]': pool.h:240:8: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from ebwt_search.cpp:21: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from alphabet.h:9, from ebwt_search.cpp:18: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Branch]': pool.h:215:7: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from ebwt_search.cpp:21: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from alphabet.h:9, from ebwt_search.cpp:18: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Branch]': pool.h:217:8: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from ebwt_search.cpp:21: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ alphabet.cpp:293:1: warning: narrowing conversion of '-1' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] }; ^ pat.cpp: In member function 'std::pair PatternSourcePerThread::nextReadPair()': pat.cpp:109:36: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] bool this_is_last = buf_.cur_buf_ == last_batch_size_-1; ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ pat.cpp: In member function 'virtual bool FastaPatternSource::parse(Read&, Read&, TReadId) const': pat.cpp:711:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for(size_t i = 0; i < seqoff - trim3; i++) { ~~^~~~~~~~~~~~~~~~ pat.cpp: In member function 'virtual bool FastaContinuousPatternSource::parse(Read&, Read&, TReadId) const': pat.cpp:888:22: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for(size_t i = 0; i < seqoff; i++) { ~~^~~~~~~~ In file included from ebwt_search_util.h:9, from ebwt_search_util.cpp:1: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from sam.cpp:12: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from hit.cpp:1: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { g++ -O0 -g3 \ -DCOMPILER_OPTIONS="\"-O0 -g3 -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now\"" -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \ -isystem /usr/include/seqan -I . \ -o bowtie-inspect-s-debug bowtie_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp \ -Wl,-z,relro -Wl,-z,now -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:162:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:163:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from ebwt.h:27, from bowtie_inspect.cpp:10: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:204:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:204:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ In file included from ebwt.h:31, from bowtie_inspect.cpp:10: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from bowtie_inspect.cpp:10: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:826:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:827:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:834:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:835:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::free(T*, uint32_t) [with T = Edit; uint32_t = unsigned int]': range_source.h:138:75: required from here pool.h:306:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, num * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'void AllocOnlyPool::free(T*) [with T = Branch]': range_source.h:789:18: required from here pool.h:286:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from bowtie_inspect.cpp:10: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Edit]': pool.h:238:7: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Edit]': pool.h:240:8: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Branch]': pool.h:215:7: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from bowtie_inspect.cpp:10: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Branch]': pool.h:217:8: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from bowtie_inspect.cpp:10: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ alphabet.cpp:293:1: warning: narrowing conversion of '-1' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] }; ^ g++ -O0 -g3 \ -DCOMPILER_OPTIONS="\"-O0 -g3 -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now\"" -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \ -isystem /usr/include/seqan -I . \ -o bowtie-inspect-l-debug bowtie_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp \ -Wl,-z,relro -Wl,-z,now -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:162:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:163:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from ebwt.h:27, from bowtie_inspect.cpp:10: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:204:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:204:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ In file included from ebwt.h:31, from bowtie_inspect.cpp:10: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:609:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { In file included from bowtie_inspect.cpp:10: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:826:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:827:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:834:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:835:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::free(T*, uint32_t) [with T = Edit; uint32_t = unsigned int]': range_source.h:138:75: required from here pool.h:306:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, num * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'void AllocOnlyPool::free(T*) [with T = Branch]': range_source.h:789:18: required from here pool.h:286:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from bowtie_inspect.cpp:10: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Edit]': pool.h:238:7: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Edit]': pool.h:240:8: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:22, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:13, from blockwise_sa.h:19, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Branch]': pool.h:215:7: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from bowtie_inspect.cpp:10: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Branch]': pool.h:217:8: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:658:35: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1654, from bowtie_inspect.cpp:10: range_source.h:516:7: note: 'class Branch' declared here class Branch { ^~~~~~ alphabet.cpp:293:1: warning: narrowing conversion of '-1' from 'int' to 'char' inside { } is ill-formed in C++11 [-Wnarrowing] }; ^ make[2]: Leaving directory '/build/bowtie-1.2.2+dfsg' make[1]: Leaving directory '/build/bowtie-1.2.2+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/bowtie-1.2.2+dfsg' $DEB_BUILD_OPTIONS is [buildinfo=+all reproducible=+all parallel=8] # print DEB_BUILD_OPTIONS ln -s debian/tests sh debian/tests/run-unit-test test_at_build_time # reads processed: 1 # reads with at least one reported alignment: 1 (100.00%) # reads that failed to align: 0 (0.00%) Reported 5 alignments example1 OK # reads processed: 1 # reads with at least one reported alignment: 1 (100.00%) # reads that failed to align: 0 (0.00%) Reported 3 alignments example2 OK # reads processed: 1 # reads with at least one reported alignment: 1 (100.00%) # reads that failed to align: 0 (0.00%) Reported 5 alignments example3 OK # reads processed: 1 # reads with at least one reported alignment: 1 (100.00%) # reads that failed to align: 0 (0.00%) Reported 1 alignments example4 OK # reads processed: 1 # reads with at least one reported alignment: 1 (100.00%) # reads that failed to align: 0 (0.00%) Reported 5 alignments example5 OK example7 OK # reads processed: 1 # reads with at least one reported alignment: 1 (100.00%) # reads that failed to align: 0 (0.00%) Reported 5 alignments example8 OK # reads processed: 1 # reads with at least one reported alignment: 1 (100.00%) # reads that failed to align: 0 (0.00%) Reported 1 alignments rm -f tests examples[0-9].out make[1]: Leaving directory '/build/bowtie-1.2.2+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_installdirs debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/bowtie-1.2.2+dfsg' # remove strange byte-compyled Python code bowtie-buildc (no idea how and why it was created) find . -name bowtie-buildc -delete find . -name .cvsignore -delete make[1]: Leaving directory '/build/bowtie-1.2.2+dfsg' dh_auto_install -Nbowtie make -j8 install DESTDIR=/build/bowtie-1.2.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bowtie-1.2.2+dfsg' mkdir -p /build/bowtie-1.2.2+dfsg/debian/tmp/usr/local/bin for file in bowtie-build-s bowtie-build-l bowtie-align-s bowtie-align-l bowtie-inspect-s bowtie-inspect-l bowtie-inspect bowtie-build bowtie ; do \ cp -f $file /build/bowtie-1.2.2+dfsg/debian/tmp/usr/local/bin ; \ done make[1]: Leaving directory '/build/bowtie-1.2.2+dfsg' dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installman-arch make[1]: Entering directory '/build/bowtie-1.2.2+dfsg' help2man --name="ultrafast memory-efficient short read aligner" --no-info \ /build/bowtie-1.2.2+dfsg/bowtie > /build/bowtie-1.2.2+dfsg/debian/bowtie/usr/share/man/man1/bowtie.1 help2man --name="building a colorspace index for bowtie" --no-info \ /build/bowtie-1.2.2+dfsg/bowtie-build > /build/bowtie-1.2.2+dfsg/debian/bowtie/usr/share/man/man1/bowtie-build.1 help2man --name="extracts information from a bowtie index" --no-info \ /build/bowtie-1.2.2+dfsg/bowtie-inspect > /build/bowtie-1.2.2+dfsg/debian/bowtie/usr/share/man/man1/bowtie-inspect.1 make[1]: Leaving directory '/build/bowtie-1.2.2+dfsg' dh_lintian dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/bowtie-1.2.2+dfsg' dh_compress -X.ebwt make[1]: Leaving directory '/build/bowtie-1.2.2+dfsg' debian/rules override_dh_fixperms-indep make[1]: Entering directory '/build/bowtie-1.2.2+dfsg' dh_fixperms chmod 644 debian/bowtie-examples/usr/share/doc/bowtie/examples/indexes/* make[1]: Leaving directory '/build/bowtie-1.2.2+dfsg' dh_fixperms -Nbowtie-examples dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'bowtie' in '../bowtie_1.2.2+dfsg-4_arm64.deb'. dpkg-deb: building package 'bowtie-dbgsym' in '../bowtie-dbgsym_1.2.2+dfsg-4_arm64.deb'. dpkg-deb: building package 'bowtie-examples' in '../bowtie-examples_1.2.2+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bowtie_1.2.2+dfsg-4_arm64.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/5915/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/5915/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/5915 and its subdirectories I: Current time: Sat Aug 28 00:12:01 +14 2021 I: pbuilder-time-stamp: 1630059121