I: pbuilder: network access will be disabled during build
I: Current time: Fri May 17 17:22:25 -12 2024
I: pbuilder-time-stamp: 1716009745
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
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 [snap-aligner_2.0.2+dfsg-1.dsc]
I: copying [./snap-aligner_2.0.2+dfsg.orig.tar.xz]
I: copying [./snap-aligner_2.0.2+dfsg-1.debian.tar.xz]
I: Extracting source
gpgv: Signature made Wed Feb 1 07:29:56 2023 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./snap-aligner_2.0.2+dfsg-1.dsc: no acceptable signature found
dpkg-source: info: extracting snap-aligner in snap-aligner-2.0.2+dfsg
dpkg-source: info: unpacking snap-aligner_2.0.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking snap-aligner_2.0.2+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying non-x86-and-kfreebsd
dpkg-source: info: applying drop-msse
dpkg-source: info: applying simde
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/3186614/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='6ae315a2526a4fe8854333fc7997dc50'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='3186614'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.arihrer6/pbuilderrc_bdsV --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.arihrer6/b1 --logfile b1/build.log snap-aligner_2.0.2+dfsg-1.dsc'
SUDO_GID='111'
SUDO_UID='106'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://85.184.249.68:3128'
I: uname -a
Linux ionos15-amd64 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux
I: ls -l /bin
total 5632
-rwxr-xr-x 1 root root 1265648 Feb 12 2023 bash
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 44016 Sep 20 2022 cat
-rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 72752 Sep 20 2022 chown
-rwxr-xr-x 1 root root 151152 Sep 20 2022 cp
-rwxr-xr-x 1 root root 125640 Jan 5 2023 dash
-rwxr-xr-x 1 root root 121904 Sep 20 2022 date
-rwxr-xr-x 1 root root 89240 Sep 20 2022 dd
-rwxr-xr-x 1 root root 102200 Sep 20 2022 df
-rwxr-xr-x 1 root root 151344 Sep 20 2022 dir
-rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname
-rwxr-xr-x 1 root root 43856 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 2023 egrep
-rwxr-xr-x 1 root root 35664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep
-rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt
-rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount
-rwxr-xr-x 1 root root 203152 Jan 24 2023 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname
-rwxr-xr-x 1 root root 72824 Sep 20 2022 ln
-rwxr-xr-x 1 root root 53024 Mar 23 2023 login
-rwxr-xr-x 1 root root 151344 Sep 20 2022 ls
-rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk
-rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 59712 Mar 22 2023 more
-rwsr-xr-x 1 root root 59704 Mar 22 2023 mount
-rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint
-rwxr-xr-x 1 root root 142968 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash
-rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 72752 Sep 20 2022 rm
-rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 126424 Jan 5 2023 sed
lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash
-rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 85008 Sep 20 2022 stty
-rwsr-xr-x 1 root root 72000 Mar 22 2023 su
-rwxr-xr-x 1 root root 39824 Sep 20 2022 sync
-rwxr-xr-x 1 root root 531984 Apr 6 2023 tar
-rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 109616 Sep 20 2022 touch
-rwxr-xr-x 1 root root 35664 Sep 20 2022 true
-rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server
-rwsr-xr-x 1 root root 35128 Mar 22 2023 umount
-rwxr-xr-x 1 root root 43888 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/3186614/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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-compat (= 13), help2man, zlib1g-dev, libsimde-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 ... 19596 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-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on help2man; however:
Package help2man is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libsimde-dev; however:
Package libsimde-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} bsdextrautils{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} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsimde-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 34 newly installed, 0 to remove and 0 not upgraded.
Need to get 20.2 MB of archives. After unpacking 81.1 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB]
Get: 2 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get: 4 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get: 5 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get: 6 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get: 7 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 8 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get: 9 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get: 11 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get: 12 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 13 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 14 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 15 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 16 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 17 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 18 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 19 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 22 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 23 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 24 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 25 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 26 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 27 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 help2man amd64 1.49.3 [198 kB]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 libsimde-dev all 0.7.4~rc2-2 [377 kB]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB]
Fetched 20.2 MB in 0s (69.2 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package liblocale-gettext-perl.
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(Reading database ... 19596 files and directories currently installed.)
Preparing to unpack .../00-liblocale-gettext-perl_1.07-5_amd64.deb ...
Unpacking liblocale-gettext-perl (1.07-5) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_amd64.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:amd64.
Preparing to unpack .../03-libmagic1_1%3a5.44-3_amd64.deb ...
Unpacking libmagic1:amd64 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../04-file_1%3a5.44-3_amd64.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../05-gettext-base_0.21-12_amd64.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../06-libuchardet0_0.0.7-1_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../07-groff-base_1.22.4-10_amd64.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_amd64.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../09-libpipeline1_1.5.7-1_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../10-man-db_2.11.2-2_amd64.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../11-m4_1.4.19-3_amd64.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../12-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../15-autopoint_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../16-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../20-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:amd64.
Preparing to unpack .../23-libelf1_0.188-2.1_amd64.deb ...
Unpacking libelf1:amd64 (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../24-dwz_0.15-1_amd64.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:amd64.
Preparing to unpack .../25-libicu72_72.1-3_amd64.deb ...
Unpacking libicu72:amd64 (72.1-3) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.1+b3_amd64.deb ...
Unpacking libxml2:amd64 (2.9.14+dfsg-1.1+b3) ...
Selecting previously unselected package gettext.
Preparing to unpack .../27-gettext_0.21-12_amd64.deb ...
Unpacking gettext (0.21-12) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../30-debhelper_13.11.4_all.deb ...
Unpacking debhelper (13.11.4) ...
Selecting previously unselected package help2man.
Preparing to unpack .../31-help2man_1.49.3_amd64.deb ...
Unpacking help2man (1.49.3) ...
Selecting previously unselected package libsimde-dev.
Preparing to unpack .../32-libsimde-dev_0.7.4~rc2-2_all.deb ...
Unpacking libsimde-dev (0.7.4~rc2-2) ...
Selecting previously unselected package zlib1g-dev:amd64.
Preparing to unpack .../33-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ...
Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ...
Setting up libpipeline1:amd64 (1.5.7-1) ...
Setting up libsimde-dev (0.7.4~rc2-2) ...
Setting up libicu72:amd64 (72.1-3) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.4) ...
Setting up libmagic1:amd64 (1:5.44-3) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up file (1:5.44-3) ...
Setting up autotools-dev (20220109.1) ...
Setting up autopoint (0.21-12) ...
Setting up autoconf (2.71-3) ...
Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ...
Setting up sensible-utils (0.0.17+nmu1) ...
Setting up libuchardet0:amd64 (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libelf1:amd64 (0.188-2.1) ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up help2man (1.49.3) ...
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Not building database; man-db/auto-update is not 'true'.
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Reading package lists...
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Writing extended state information...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/snap-aligner-2.0.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../snap-aligner_2.0.2+dfsg-1_source.changes
dpkg-buildpackage: info: source package snap-aligner
dpkg-buildpackage: info: source version 2.0.2+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/snap-aligner-2.0.2+dfsg'
dh_auto_clean
make -j16 clean
make[2]: Entering directory '/build/snap-aligner-2.0.2+dfsg'
rm -f SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o snap-aligner unit_tests SNAPCommand snap SNAP
make[2]: Leaving directory '/build/snap-aligner-2.0.2+dfsg'
rm -f debian/*.1
rm -f */*.d */*/*.d
make[1]: Leaving directory '/build/snap-aligner-2.0.2+dfsg'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/snap-aligner-2.0.2+dfsg'
dh_auto_build
make -j16 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/snap-aligner-2.0.2+dfsg'
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGap.o SNAPLib/AffineGap.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGapVectorized.o SNAPLib/AffineGapVectorized.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerContext.o SNAPLib/AlignerContext.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerOptions.o SNAPLib/AlignerOptions.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerStats.o SNAPLib/AlignerStats.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentAdjuster.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentResult.o SNAPLib/AlignmentResult.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ApproximateCounter.o SNAPLib/ApproximateCounter.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Bam.o SNAPLib/Bam.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BaseAligner.o SNAPLib/BaseAligner.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BigAlloc.o SNAPLib/BigAlloc.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BufferedAsync.o SNAPLib/BufferedAsync.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ChimericPairedEndAligner.o SNAPLib/ChimericPairedEndAligner.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/CommandProcessor.o SNAPLib/CommandProcessor.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Compat.o SNAPLib/Compat.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataReader.o SNAPLib/DataReader.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataWriter.o SNAPLib/DataWriter.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Error.o SNAPLib/Error.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTA.o SNAPLib/FASTA.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTQ.o SNAPLib/FASTQ.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp
SNAPLib/DataReader.cpp: In static member function 'static bool DecompressDataReader::decompress(z_stream*, ThreadHeap*, char*, _int64, _int64*, char*, _int64, _int64*, DecompressMode)':
SNAPLib/DataReader.cpp:2012:53: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=]
2012 | fprintf(stderr, "\n0x%llx\t", offset);
| ~~~^ ~~~~~~
| | |
| | _int64 {aka long int}
| long long unsigned int
| %lx
SNAPLib/DataReader.cpp: In member function 'char* DecompressDataReader::findPointer(void*)':
SNAPLib/DataReader.cpp:2065:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=]
2065 | sprintf(result, "compressed #%d @ %lld", i, (char*)p - e->compressed);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int long int
| %ld
SNAPLib/DataReader.cpp:2069:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=]
2069 | sprintf(result, "decompressed #%d %lld", i, (char*) p - e->decompressed);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int long int
| %ld
SNAPLib/DataReader.cpp:2073:43: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=]
2073 | sprintf(result, "extra #%d %lld", i, (char*) p - e->decompressed - extraBytes);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int long int
| %ld
SNAPLib/DataReader.cpp: In static member function 'static void DecompressDataReader::decompressThread(void*)':
SNAPLib/DataReader.cpp:2221:174: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=]
2221 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int _int64 {aka long int}
| %ld
SNAPLib/DataReader.cpp:2221:198: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=]
2221 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry);
| ~~~^ ~~~~~~
| | |
| long long int _int64 {aka long int}
| %ld
SNAPLib/DataReader.cpp:2225:74: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=]
2225 | fprintf(stderr, "error reading BAM file at offset %lld\n", reader->getFileOffset());
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int _int64 {aka long int}
| %ld
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_Blob.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_HDFS.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_map.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_stdio.o SNAPLib/GenericFile_stdio.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Genome.o SNAPLib/Genome.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenomeIndex.o SNAPLib/GenomeIndex.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HashTable.o SNAPLib/HashTable.cpp
SNAPLib/Error.cpp: In function 'void WriteProgressCounter(const char*, _int64)':
SNAPLib/Error.cpp:96:49: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=]
96 | fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment);
| ~~~^ ~~~~~~~~~
| | |
| long long int _int64 {aka long int}
| %ld
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Histogram.o SNAPLib/Histogram.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HitDepth.o SNAPLib/HitDepth.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp
SNAPLib/Genome.cpp: In member function 'bool Genome::saveToFile(const char*) const':
SNAPLib/Genome.cpp:216:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'long int' [-Wformat=]
216 | fprintf(saveFile,"%lld %d %d\n",nBases, nContigs, GENOME_FLAG_ALT_CONTIGS_MARKED);
| ~~~^ ~~~~~~
| | |
| | long int
| long long int
| %ld
SNAPLib/Genome.cpp:226:31: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=]
226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation),
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int _int64 {aka long int}
| %ld
SNAPLib/Genome.cpp:226:42: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_int64' {aka 'long int'} [-Wformat=]
226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation),
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int _int64 {aka long int}
| %ld
SNAPLib/Genome.cpp: In static member function 'static const Genome* Genome::loadFromFile(const char*, unsigned int, GenomeLocation, GenomeDistance, bool)':
SNAPLib/Genome.cpp:356:47: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type '_int64*' {aka 'long int*'} [-Wformat=]
356 | if (7 != sscanf(contigNameBuffer, "%lld %x %d %lld %x %d %d", &contigStart, &flags, &originalContigNumber, &projContigStart, &altProjRC, &contigNameSize, &cigarLength)) {
| ~~~^ ~~~~~~~~~~~~
| | |
| long long int* _int64* {aka long int*}
| %ld
SNAPLib/Genome.cpp:356:58: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=]
356 | if (7 != sscanf(contigNameBuffer, "%lld %x %d %lld %x %d %d", &contigStart, &flags, &originalContigNumber, &projContigStart, &altProjRC, &contigNameSize, &cigarLength)) {
| ~~~^ ~~~~~~~~~~~~~~~~
| | |
| long long int* _int64* {aka long int*}
| %ld
SNAPLib/Genome.cpp: In static member function 'static bool Genome::openFileAndGetSizes(const char*, GenericFile**, GenomeDistance*, unsigned int*, bool)':
SNAPLib/Genome.cpp:497:51: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=]
497 | if (NULL == retval || 3 != sscanf(linebuf,"%lld %d %d\n", nBases, nContigs, &flags)) {
| ~~~^ ~~~~~~
| | |
| | GenomeDistance* {aka long int*}
| long long int*
| %ld
SNAPLib/GenomeIndex.cpp: In static member function 'static bool GenomeIndex::BuildIndexToDirectory(const Genome*, int, double, const char*, unsigned int, unsigned int, bool, unsigned int, bool, const char*, unsigned int, bool)':
SNAPLib/GenomeIndex.cpp:952:36: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=]
952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int _uint64 {aka long unsigned int}
| %ld
SNAPLib/GenomeIndex.cpp:952:61: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type '_uint64' {aka 'long unsigned int'} [-Wformat=]
952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long int _uint64 {aka long unsigned int}
| %ld
SNAPLib/GenomeIndex.cpp:952:103: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=]
952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed);
| ~~~^ ~~~~~~~~~~~
| | |
| long long int _uint64 {aka long unsigned int}
| %ld
SNAPLib/GenomeIndex.cpp:1007:36: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=]
1007 | fprintf(indexFile,"%d %d %d %lld %d %d %d %lld %d %d", GenomeIndexFormatMajorVersion, GenomeIndexFormatMinorVersion, index->nHashTables,
| ~~~^
| |
| long long int
| %ld
1008 | index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize);
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| _uint64 {aka long unsigned int}
SNAPLib/GenomeIndex.cpp:1007:50: warning: format '%lld' expects argument of type 'long long int', but argument 10 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
1007 | fprintf(indexFile,"%d %d %d %lld %d %d %d %lld %d %d", GenomeIndexFormatMajorVersion, GenomeIndexFormatMinorVersion, index->nHashTables,
| ~~~^
| |
| long long int
| %ld
1008 | index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize);
| ~~~~~~~~~~~~~~~~~
| |
| size_t {aka long unsigned int}
SNAPLib/GenomeIndex.cpp: In static member function 'static GenomeIndex* GenomeIndex::loadFromDirectory(char*, bool, bool)':
SNAPLib/GenomeIndex.cpp:1879:57: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=]
1879 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding,
| ~~~^ ~~~~~~~~~~~~~~~~~~
| | |
| long long int* _int64* {aka long int*}
| %ld
SNAPLib/GenomeIndex.cpp:1879:71: warning: format '%lld' expects argument of type 'long long int*', but argument 10 has type 'size_t*' {aka 'long unsigned int*'} [-Wformat=]
1879 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding,
| ~~~^
| |
| long long int*
| %ld
1880 | &hashTableKeySize, &hashTablesFileSize, &smallHashTable, &locationSize))) {
| ~~~~~~~~~~~~~~~~~~~
| |
| size_t* {aka long unsigned int*}
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp
In file included from SNAPLib/IntersectingPairedEndAligner.cpp:24:
SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions]
767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} };
| ^
SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions]
767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} };
| ^
In file included from SNAPLib/PairedAligner.cpp:47:
SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions]
767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} };
| ^
SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions]
767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} };
| ^
SNAPLib/PairedAligner.cpp: In member function 'void PairedAlignerContext::runIterationThreadImpl(Read**)':
SNAPLib/PairedAligner.cpp:673:72: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
673 | fprintf(stderr, "reporter:counter:SNAP,readsAligned,%llu\n", stats->totalReads - readsWhenLastReported);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int long unsigned int
| %lu
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadSupplierQueue.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Seed.o SNAPLib/Seed.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Tables.o SNAPLib/Tables.cpp
SNAPLib/ReadReader.cpp: In member function 'virtual bool SimpleReadReader::getNextRead(Read*, AlignmentResult*, unsigned int*, bool*, unsigned int*, unsigned int*, const char**)':
SNAPLib/ReadReader.cpp:44:5: warning: no return statement in function returning non-void [-Wreturn-type]
44 | }
| ^
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Util.o SNAPLib/Util.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/exit.o SNAPLib/exit.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/mapq.o SNAPLib/mapq.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/stdafx.o SNAPLib/stdafx.cpp
SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeHeader(const ReaderContext&, char*, size_t, size_t*, bool, int, const char**, const char*, const char*, bool) const':
SNAPLib/SAM.cpp:1292:116: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'long int' [-Wformat=]
1292 | bytesConsumed += snprintf(header + bytesConsumed, headerBufferSize - bytesConsumed, "@SQ\tSN:%s\tLN:%llu%s\n", contig->name, contig->length - context.genome->getChromosomePadding(), contig->isALT ? "\tAH:*":"");
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int long int
| %lu
SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writePairs(const ReaderContext&, LandauVishkinWithCigar*, AffineGapVectorizedWithCigar*, bool, char*, size_t, size_t*, size_t*, Read**, GenomeLocation*, PairedAlignmentResult*, bool, bool, char*, bool, int*, int*, bool*, bool*) const':
SNAPLib/SAM.cpp:1854:77: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
1854 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%s%s%.*s\n",
| ~~~^
| |
| long long unsigned int
| %lu
......
1858 | positionInContig[whichRead],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| GenomeDistance {aka long int}
SNAPLib/SAM.cpp:1854:95: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
1854 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%s%s%.*s\n",
| ~~~^
| |
| long long unsigned int
| %lu
......
1862 | matePositionInContig[whichRead],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| GenomeDistance {aka long int}
SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, LandauVishkinWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, bool, int*, int, bool, char*, bool, _int64, int, int, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool, int, int) const':
SNAPLib/SAM.cpp:2076:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n",
| ~~~^
| |
| long long unsigned int
| %lu
......
2080 | positionInContig,
| ~~~~~~~~~~~~~~~~
| |
| GenomeDistance {aka long int}
SNAPLib/SAM.cpp:2076:91: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n",
| ~~~^
| |
| long long unsigned int
| %lu
......
2084 | matePositionInContig,
| ~~~~~~~~~~~~~~~~~~~~
| |
| GenomeDistance {aka long int}
SNAPLib/SAM.cpp:2076:97: warning: format '%lld' expects argument of type 'long long int', but argument 13 has type '_int64' {aka 'long int'} [-Wformat=]
2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n",
| ~~~^
| |
| long long int
| %ld
......
2085 | templateLength,
| ~~~~~~~~~~~~~~
| |
| _int64 {aka long int}
SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, AffineGapVectorizedWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, bool, int*, int, int, bool, char*, bool, _int64, int, int, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool, int, int) const':
SNAPLib/SAM.cpp:2312:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n",
| ~~~^
| |
| long long unsigned int
| %lu
......
2316 | positionInContig,
| ~~~~~~~~~~~~~~~~
| |
| GenomeDistance {aka long int}
SNAPLib/SAM.cpp:2312:91: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n",
| ~~~^
| |
| long long unsigned int
| %lu
......
2320 | matePositionInContig,
| ~~~~~~~~~~~~~~~~~~~~
| |
| GenomeDistance {aka long int}
SNAPLib/SAM.cpp:2312:97: warning: format '%lld' expects argument of type 'long long int', but argument 13 has type '_int64' {aka 'long int'} [-Wformat=]
2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n",
| ~~~^
| |
| long long int
| %ld
......
2321 | templateLength,
| ~~~~~~~~~~~~~~
| |
| _int64 {aka long int}
SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)':
SNAPLib/SAM.cpp:2650:58: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int GenomeDistance {aka long int}
| %lu
SNAPLib/SAM.cpp:2654:56: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2654 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int GenomeDistance {aka long int}
| %lu
SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)':
SNAPLib/SAM.cpp:2745:58: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int GenomeDistance {aka long int}
| %lu
SNAPLib/SAM.cpp:2749:56: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=]
2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int GenomeDistance {aka long int}
| %lu
SNAPLib/SAM.cpp: In static member function 'static void SAMFormat::printRead(const Genome*, Read*, GenomeLocation)':
SNAPLib/SAM.cpp:2820:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'GenomeLocation' {aka 'long int'} [-Wformat=]
2820 | printf("Aligned location %s:%llu\n",
| ~~~^
| |
| long long unsigned int
| %lu
2821 | genome->getContigAtLocation(location)->name,
2822 | location - genome->getContigAtLocation(location)->beginningLocation);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| GenomeLocation {aka long int}
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp
SNAPLib/SingleAligner.cpp: In member function 'virtual void SingleAlignerContext::runIterationThreadImpl(Read*&)':
SNAPLib/SingleAligner.cpp:207:67: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
207 | fprintf(stderr,"reporter:counter:SNAP,readsAligned,%llu\n",stats->totalReads - readsWhenLastReported);
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int long unsigned int
| %lu
SNAPLib/Util.cpp: In function 'char* FormatUIntWithCommas(_uint64, char*, size_t, size_t)':
SNAPLib/Util.cpp:167:49: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=]
167 | sprintf(tempBuf, ",%03lld", x % 1000);
| ~~~~~^ ~~~~~~~~
| | |
| | _uint64 {aka long unsigned int}
| long long int
| %03ld
SNAPLib/Util.cpp:170:46: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=]
170 | sprintf(tempBuf, "%lld", x);
| ~~~^ ~
| | |
| | _uint64 {aka long unsigned int}
| long long int
| %ld
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/stdafx.o apps/snap/stdafx.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapVectorizedTest.o tests/AffineGapVectorizedTest.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/TestLib.o tests/TestLib.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/main.o tests/main.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/SNAPCommand.cpp
g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp
SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)':
SNAPLib/SAM.cpp:2650:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=]
2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore);
| ^~~~
SNAPLib/SAM.cpp:2650:54: note: directive argument in the range [1, 9223372036854775807]
2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore);
| ^~~~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/fstream:41,
from SNAPLib/stdafx.h:14,
from SNAPLib/SAM.cpp:19:
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2650:21:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16
54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
55 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)':
SNAPLib/SAM.cpp:2654:53: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=]
2654 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter);
| ^~~~
SNAPLib/SAM.cpp:2654:52: note: directive argument in the range [1, 9223372036854775807]
2654 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter);
| ^~~~~~~
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2654:21:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16
54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
55 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)':
SNAPLib/SAM.cpp:2745:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=]
2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore);
| ^~~~
SNAPLib/SAM.cpp:2745:54: note: directive argument in the range [1, 9223372036854775807]
2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore);
| ^~~~~~~
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2745:21:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16
54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
55 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)':
SNAPLib/SAM.cpp:2749:53: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=]
2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter);
| ^~~~
SNAPLib/SAM.cpp:2749:52: note: directive argument in the range [1, 9223372036854775807]
2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter);
| ^~~~~~~
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2749:21:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16
54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
55 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -o snap-aligner -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o -lrt -lz
echo SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o
SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o
echo SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o
SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o
g++ -o SNAPCommand -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o -lrt -lz
g++ -o unit_tests -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o -lrt -lz
make[2]: Leaving directory '/build/snap-aligner-2.0.2+dfsg'
help2man --no-discard-stderr --no-info --version-string="2.0.2" \
--name "scalable nucleotide alignment program" \
--help-option=" " ./snap-aligner > debian/snap-aligner.1
for option in index single paired; do help2man \
--no-discard-stderr --no-info --version-string="2.0.2" \
--include=debian/snap-aligner-${option}-man-include \
--help-option=" " "./snap-aligner ${option}" > \
debian/snap-aligner-${option}.1; done
help2man --no-discard-stderr --no-info --version-string="2.0.2" \
--name "scalable nucleotide alignment program" \
--help-option=" " ./SNAPCommand > debian/SNAPCommand.1
make[1]: Leaving directory '/build/snap-aligner-2.0.2+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/snap-aligner-2.0.2+dfsg'
dh_auto_test
./unit_tests
AffineGapTest:
- synthetic: [OK]
AffineGapVectorizedTest:
- equal strings: [OK]
- one deletion: [OK]
- long deletion: [OK]
- long insertion: [OK]
- synthetic: [OK]
EventTest:
- many waiters: [OK]
- single waiters: [OK]
LandauVishkinTest:
- equal strings: [OK]
- prefixes: [OK]
- non-equal strings: [OK]
- overly distant strings: [OK]
- CIGAR strings: [OK]
ProbabilityDistanceTest:
- basic probabilities: [OK]
- indels: [OK]
15 / 15 tests passed.
make[1]: Leaving directory '/build/snap-aligner-2.0.2+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/snap-aligner/
dh_install
dh_installdocs
dh_installchangelogs
dh_installexamples
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'snap-aligner' in '../snap-aligner_2.0.2+dfsg-1_amd64.deb'.
dpkg-deb: building package 'snap-aligner-dbgsym' in '../snap-aligner-dbgsym_2.0.2+dfsg-1_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../snap-aligner_2.0.2+dfsg-1_amd64.buildinfo
dpkg-genchanges --build=binary -O../snap-aligner_2.0.2+dfsg-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
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/3186614 and its subdirectories
I: Current time: Fri May 17 17:25:15 -12 2024
I: pbuilder-time-stamp: 1716009915