I: pbuilder: network access will be disabled during build
I: Current time: Mon Mar 10 12:51:36 +14 2025
I: pbuilder-time-stamp: 1741560696
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-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: using eatmydata during job
I: Copying source file
I: copying [wham-align_0.1.5-8.dsc]
I: copying [./wham-align_0.1.5.orig.tar.gz]
I: copying [./wham-align_0.1.5-8.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./wham-align_0.1.5-8.dsc: unsupported subcommand
dpkg-source: info: extracting wham-align in wham-align-0.1.5
dpkg-source: info: unpacking wham-align_0.1.5.orig.tar.gz
dpkg-source: info: unpacking wham-align_0.1.5-8.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying makefile.patch
dpkg-source: info: applying non-x86.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying cross-build.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/38356/tmp/hooks/D01_modify_environment starting
debug: Running on ionos2-i386.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Mar 9 22:51 /bin/sh -> /bin/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/38356/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/38356/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=i386
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 '
DIRSTACK=()
DISTRIBUTION=trixie
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=i686
HOST_ARCH=i386
IFS='
'
INVOCATION_ID=cd8f5050977d49bcb438464ac902aed1
LANG=C
LANGUAGE=de_CH:de
LC_ALL=C
LD_LIBRARY_PATH=/usr/lib/libeatmydata
LD_PRELOAD=libeatmydata.so
MACHTYPE=i686-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=38356
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/r-b-build.ivKiNFlH/pbuilderrc_rTr5 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ivKiNFlH/b2 --logfile b2/build.log wham-align_0.1.5-8.dsc'
SUDO_GID=112
SUDO_UID=107
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://46.16.76.132:3128
I: uname -a
Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/38356/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: i386
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)
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19787 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.
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} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{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, 30 newly installed, 0 to remove and 0 not upgraded.
Need to get 20.8 MB of archives. After unpacking 78.2 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-5 [96.5 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-7 [301 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-3 [539 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 22 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b2 [734 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB]
Fetched 20.8 MB in 0s (52.1 MB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19787 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:i386.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic1t64:i386 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.45-3+b1_i386.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.23.1-1_i386.deb ...
Unpacking gettext-base (0.23.1-1) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_i386.deb ...
Unpacking libuchardet0:i386 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.23.0-7_i386.deb ...
Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.40.4-5_i386.deb ...
Unpacking bsdextrautils (2.40.4-5) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../08-libpipeline1_1.5.8-1_i386.deb ...
Unpacking libpipeline1:i386 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.13.0-1_i386.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-7_i386.deb ...
Unpacking m4 (1.4.19-7) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ...
Unpacking automake (1:1.17-3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ...
Unpacking autopoint (0.23.1-1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ...
Unpacking libdebhelper-perl (13.24.1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.5.4-3_all.deb ...
Unpacking libtool (2.5.4-3) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../17-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.1-2) ...
Selecting previously unselected package libelf1t64:i386.
Preparing to unpack .../21-libelf1t64_0.192-4_i386.deb ...
Unpacking libelf1t64:i386 (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../22-dwz_0.15-1+b1_i386.deb ...
Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package libunistring5:i386.
Preparing to unpack .../23-libunistring5_1.3-1_i386.deb ...
Unpacking libunistring5:i386 (1.3-1) ...
Selecting previously unselected package libicu72:i386.
Preparing to unpack .../24-libicu72_72.1-6_i386.deb ...
Unpacking libicu72:i386 (72.1-6) ...
Selecting previously unselected package libxml2:i386.
Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_i386.deb ...
Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.23.1-1_i386.deb ...
Unpacking gettext (0.23.1-1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../29-debhelper_13.24.1_all.deb ...
Unpacking debhelper (13.24.1) ...
Setting up libpipeline1:i386 (1.5.8-1) ...
Setting up libicu72:i386 (72.1-6) ...
Setting up bsdextrautils (2.40.4-5) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.24.1) ...
Setting up libmagic1t64:i386 (1:5.45-3+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-7) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:i386 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libunistring5:i386 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:i386 (0.0.8-1+b2) ...
Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.24.1) ...
Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/38356/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for trixie
I: user script /srv/workspace/pbuilder/38356/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/wham-align-0.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../wham-align_0.1.5-8_source.changes
dpkg-buildpackage: info: source package wham-align
dpkg-buildpackage: info: source version 0.1.5-8
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <npatra974@gmail.com>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean
dh_auto_clean
make -j10 clean
make[1]: Entering directory '/build/reproducible-path/wham-align-0.1.5'
rm -f wham wham-build *.o
make[1]: Leaving directory '/build/reproducible-path/wham-align-0.1.5'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/wham-align.substvars debian/files
rm -fr -- debian/wham-align/ debian/tmp/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j10 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/wham-align-0.1.5'
g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hash.cpp
g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings embedhash.cpp
g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings main.cpp
g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings sequence.cpp
g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings aligner.cpp
g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings interval.cpp
g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings edit_distance.cpp
g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings error.cpp
g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings short.cpp
g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hitset.cpp
error.cpp: In function 'void elog(int, char*, ...)':
error.cpp:31:9: warning: unused variable 'filename' [-Wunused-variable]
31 | char *filename = __FILE__;
| ^~~~~~~~
error.cpp:32:7: warning: unused variable 'lineno' [-Wunused-variable]
32 | int lineno = __LINE__;
| ^~~~~~
g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings perfcounters.cpp
g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings model.cpp
short.cpp: In member function 'int ShortRead::preProcess(int)':
short.cpp:212:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
212 | while (len = readLine(file, str, 256)) {
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
short.cpp: In member function 'ShortRead** ShortRead::split(int)':
short.cpp:483:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
483 | if (szPartition <= nRead - curRead)
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
interval.cpp: In constructor 'IntervalTree::IntervalTree(uint32, uint32)':
interval.cpp:67:21: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
67 | for (int i = 0; i < numLevel - 1; i++) {
| ~~^~~~~~~~~~~~~~
interval.cpp: In member function 'int IntervalTree::save(char*)':
interval.cpp:304:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
304 | if (ret != numLEntry) {
| ~~~~^~~~~~~~~~~~
interval.cpp:310:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
310 | if (ret != numIEntry) {
| ~~~~^~~~~~~~~~~~
interval.cpp: In member function 'int IntervalTree::load(char*)':
interval.cpp:359:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
359 | if (ret != numLEntry) {
| ~~~~^~~~~~~~~~~~
interval.cpp:370:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
370 | if (ret != numIEntry) {
| ~~~~^~~~~~~~~~~~
In file included from hitset.h:31,
from hitset.cpp:1:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
hitset.cpp: In member function 'int HitPairSet::build(HitSet*, HitSet*, uint32, uint32, bool (*)[2], bool)':
hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable]
90 | bool pairMatch = false;
| ^~~~~~~~~
model.cpp: In static member function 'static int AlignerModel::estimateNumPartition(unsigned int, int, int, bool)':
model.cpp:76:16: warning: variable 'nIndex' set but not used [-Wunused-but-set-variable]
76 | unsigned int nIndex, nLookup, nBucket;
| ^~~~~~
model.cpp: In static member function 'static unsigned int AlignerModel::getFreeMemory()':
model.cpp:166:28: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=]
166 | fscanf(file, "MemTotal: %d kB\n", &memTotal);
| ~^ ~~~~~~~~~
| | |
| int* unsigned int*
| %d
model.cpp:167:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=]
167 | fscanf(file, "MemFree: %d kB\n", &memFree);
| ~^ ~~~~~~~~
| | |
| int* unsigned int*
| %d
model.cpp:168:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=]
168 | fscanf(file, "Buffers: %d kB\n", &memBuffer);
| ~^ ~~~~~~~~~~
| | |
| int* unsigned int*
| %d
model.cpp:169:26: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=]
169 | fscanf(file, "Cached: %d kB\n", &memCache);
| ~^ ~~~~~~~~~
| | |
| int* unsigned int*
| %d
model.cpp: In static member function 'static unsigned int AlignerModel::estimateHashtableSpace(unsigned int, int, int, int)':
model.cpp:198:26: warning: variable 'p2' set but not used [-Wunused-but-set-variable]
198 | double nSpace, p0, p1, p2;
| ^~
In file included from hitset.h:31,
from hash.h:29,
from aligner.h:25,
from aligner.cpp:25:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
In file included from hitset.h:31,
from hash.h:29,
from embedhash.cpp:27:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
short.cpp: In member function 'int ShortRead::load(int)':
short.cpp:424:28: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized]
424 | forward_word = (forward_word << BITS_PER_BASE) | code;
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
short.cpp:310:38: note: 'code' was declared here
310 | int64 forward_word, backward_word, code;
| ^~~~
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
hash.h: In function 'uint32 murmurHash(int64*, uint32)':
hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable]
86 | uint32 sum = 0;
| ^~~
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
hash.h: In function 'uint32 murmurHash(int64*, uint32)':
hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable]
86 | uint32 sum = 0;
| ^~~
edit_distance.cpp: In function 'scoreinfo edit_distance(char*, char*, int, int, char*, char*, int)':
edit_distance.cpp:61:7: warning: unused variable 'i' [-Wunused-variable]
61 | int i;
| ^
edit_distance.cpp: In function 'scoreinfo edit_distance_align(int**, char**, char*, char*, int, int, char*, char*, int)':
edit_distance.cpp:181:10: warning: unused variable 'tmp_trace' [-Wunused-variable]
181 | char tmp_trace = traceback[i][j];
| ^~~~~~~~~
edit_distance.cpp:132:14: warning: unused variable 'x' [-Wunused-variable]
132 | int k = 0, x = 0, y = 0;
| ^
edit_distance.cpp:132:21: warning: unused variable 'y' [-Wunused-variable]
132 | int k = 0, x = 0, y = 0;
| ^
edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable]
178 | int kk = 0;
| ^~
In file included from hitset.h:31,
from hash.h:29,
from hash.cpp:27:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
hash.h: In function 'uint32 murmurHash(int64*, uint32)':
hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable]
86 | uint32 sum = 0;
| ^~~
short.cpp: In member function 'ShortRead** ShortRead::split(int)':
short.cpp:503:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=]
503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i);
| ^~
short.cpp:503:42: note: directive argument in the range [0, 1073741823]
503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i);
| ^~~~~~~~
short.cpp:503:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256
503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
short.cpp:510:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=]
510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i);
| ^~
short.cpp:510:42: note: directive argument in the range [0, 1073741823]
510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i);
| ^~~~~~~~
short.cpp:510:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256
510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings writer.cpp
g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings builder.cpp
In file included from hitset.h:31,
from hash.h:29,
from aligner.h:25,
from main.cpp:34:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
hash.h: In function 'uint32 murmurHash(int64*, uint32)':
hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable]
86 | uint32 sum = 0;
| ^~~
In file included from hitset.h:31,
from hash.h:29,
from aligner.h:25,
from sequence.cpp:30:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
aligner.cpp: In member function 'int Aligner::initLookupArray()':
aligner.cpp:365:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
365 | if ((indexBits[i] >> j) & 0x1 == 1) {
| ~~~~^~~~
aligner.cpp:371:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
371 | if ((indexBits[i] >> j) & 0x1 == 1) {
| ~~~~^~~~
embedhash.cpp: In member function 'int EmbedHashTable::preProcessEnd()':
embedhash.cpp:137:16: warning: unused variable 'ln2' [-Wunused-variable]
137 | const double ln2 = log(2);
| ^~~
embedhash.cpp: In member function 'void EmbedHashTable::setScanThreshold(double)':
embedhash.cpp:253:9: warning: unused variable 'sum' [-Wunused-variable]
253 | int64 sum = 0;
| ^~~
embedhash.cpp:255:9: warning: unused variable 'top' [-Wunused-variable]
255 | int64 top = total - total * r;
| ^~~
aligner.cpp: In member function 'int Aligner::preProcessHashTables()':
aligner.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
534 | for (i = 0; i < nHashTable; i++) {
| ~~^~~~~~~~~~~~
embedhash.cpp: In member function 'void EmbedHashTable::insert(int64*, unsigned int)':
embedhash.cpp:369:38: warning: operation on '*(((EmbedHashTable*)this)->EmbedHashTable::overflowPool + ((sizetype)(curOverflowEntry * 4)))' may be undefined [-Wsequence-point]
369 | overflowPool[curOverflowEntry] =
embedhash.cpp:328:10: warning: unused variable 'seqOffset' [-Wunused-variable]
328 | uint32 seqOffset;
| ^~~~~~~~~
embedhash.cpp:330:10: warning: unused variable 'counter' [-Wunused-variable]
330 | uint32 counter = 0;
| ^~~~~~~
embedhash.cpp:331:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable]
331 | int64 * seqVector;
| ^~~~~~~~~
embedhash.cpp:333:11: warning: unused variable 'target' [-Wunused-variable]
333 | int64 * target = &tspace[8];
| ^~~~~~
embedhash.cpp:334:8: warning: unused variable 'isBloomFilter' [-Wunused-variable]
334 | bool isBloomFilter;
| ^~~~~~~~~~~~~
embedhash.cpp:335:12: warning: unused variable 'bloomFilter' [-Wunused-variable]
335 | uint32 * bloomFilter;
| ^~~~~~~~~~~
embedhash.cpp:336:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable]
336 | uint32 bloomFilterNum;
| ^~~~~~~~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
embedhash.cpp: In member function 'unsigned int EmbedHashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)':
embedhash.cpp:385:7: warning: unused variable 'num' [-Wunused-variable]
385 | int num;
| ^~~
pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
embedhash.cpp:387:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable]
387 | uint32 seqOffset, entryOffset, startOffset;
| ^~~~~~~~~~~
embedhash.cpp:389:11: warning: unused variable 'diff' [-Wunused-variable]
389 | int64 * diff = &tspace1[8], *target = &tspace2[8];
| ^~~~
pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
embedhash.cpp:392:10: warning: unused variable 'sid' [-Wunused-variable]
392 | uint32 sid, soffset;
| ^~~
pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
embedhash.cpp:392:15: warning: unused variable 'soffset' [-Wunused-variable]
392 | uint32 sid, soffset;
| ^~~~~~~
aligner.cpp:712:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
712 | for (i = 0; i < nHashTable; i++) {
| ~~^~~~~~~~~~~~
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
aligner.cpp: In member function 'int Aligner::build(char*)':
aligner.cpp:724:16: warning: unused variable 'i' [-Wunused-variable]
724 | unsigned int i, j;
| ^
aligner.cpp:724:19: warning: unused variable 'j' [-Wunused-variable]
724 | unsigned int i, j;
| ^
aligner.cpp: In member function 'int Aligner::buildHashTables(char*)':
aligner.cpp:807:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
807 | for (i = 0; i < nHashTable; i++) {
| ~~^~~~~~~~~~~~
aligner.cpp:844:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
844 | for (i1 = 0; i1 < lenPartition * (nPartition - 1); i1 += lenPartition) {
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:864:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
864 | for (i1 = 0; i1 < lenPartition * (nPartition - 2); i1 += lenPartition) {
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:871:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
871 | for (i2 = i1; i2 < lenPartition * (nPartition - 2);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:894:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
894 | for (i1 = 0; i1 < lenPartition * (nPartition - 3); i1 += lenPartition) {
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:901:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
901 | for (i2 = i1; i2 < lenPartition * (nPartition - 3);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp: In function 'int getArguVal(char*)':
main.cpp:159:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
159 | else if (*c = 'g' || *c == 'G')
| ~~~^~~~~~~~~~~~~~~~~~
aligner.cpp:909:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
909 | for (i3 = i2; i3 < lenPartition * (nPartition - 3);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
aligner.cpp:928:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
928 | for (i1 = 0; i1 < lenPartition * (nPartition - 4); i1 += lenPartition) {
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:930:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
930 | for (i2 = i1; i2 < lenPartition * (nPartition - 4);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:933:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
933 | for (i3 = i2; i3 < lenPartition * (nPartition - 4);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:936:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
936 | for (i4 = i3; i4 < lenPartition * (nPartition - 4); i4 +=
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:951:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
951 | for (i1 = 0; i1 < lenPartition * (nPartition - 5); i1 += lenPartition) {
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:953:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
953 | for (i2 = i1; i2 < lenPartition * (nPartition - 5);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:956:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
956 | for (i3 = i2; i3 < lenPartition * (nPartition - 5);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:959:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
959 | for (i4 = i3; i4 < lenPartition * (nPartition - 5); i4 +=
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:962:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
962 | for (i5 = i4; i5 < lenPartition * (nPartition - 5); i5 +=
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
aligner.cpp:983:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
983 | for (i = 0; i < nHashTable; i++) {
| ~~^~~~~~~~~~~~
aligner.cpp:1006:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
1006 | for (i = 0; i < nHashTable; i++) {
| ~~^~~~~~~~~~~~
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)':
aligner.cpp:1035:10: warning: unused variable 'offset' [-Wunused-variable]
1035 | uint32 offset;
| ^~~~~~
aligner.cpp:1039:7: warning: unused variable 'nHit' [-Wunused-variable]
1039 | int nHit = 0;
| ^~~~
main.cpp: In function 'int align(char*, AlignInfo*, char*, int)':
main.cpp:350:7: warning: unused variable 'i' [-Wunused-variable]
350 | int i, j, ret;
| ^
main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable]
350 | int i, j, ret;
| ^
aligner.cpp: In member function 'unsigned int Aligner::align(int64*, char*, strand, int, HitSet*, bool, bool)':
aligner.cpp:1119:10: warning: variable 'offset' set but not used [-Wunused-but-set-variable]
1119 | uint32 offset;
| ^~~~~~
aligner.cpp:1123:7: warning: variable 'nHit' set but not used [-Wunused-but-set-variable]
1123 | int nHit = 0;
| ^~~~
hash.h: In function 'uint32 murmurHash(int64*, uint32)':
hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable]
86 | uint32 sum = 0;
| ^~~
aligner.cpp: In member function 'int Aligner::check(int)':
aligner.cpp:1436:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
1436 | for (i = 0; i < num; i++) {
| ~~^~~~~
aligner.cpp:1452:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
1452 | for (j = 0; j < nError; j++) {
| ~~^~~~~~~~
aligner.cpp:1426:7: warning: unused variable 'ret' [-Wunused-variable]
1426 | int ret;
| ^~~
aligner.cpp: In member function 'AlignRes Aligner::alignSingleEnd(AlignInfo*, char*)':
aligner.cpp:1541:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
1541 | for (i = 0; i < nHashTable; i++) {
| ~~^~~~~~~~~~~~
main.cpp: In function 'int main(int, char**)':
main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable]
523 | int numKeys;
| ^~~~~~~
aligner.cpp:1547:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
1547 | for (i = 0; i < res.nRead; i++) {
| ~~^~~~~~~~~~~
main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable]
526 | int nSeq = 1;
| ^~~~
main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable]
532 | CompactSequence * sequence;
| ^~~~~~~~
main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable]
534 | pthread_t * threadpool;
| ^~~~~~~~~~
main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable]
536 | int * threadid;
| ^~~~~~~~
aligner.cpp:1629:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
1629 | delete writer;
| ^~~~~~~~~~~~~
aligner.cpp:1502:10: warning: unused variable 'file' [-Wunused-variable]
1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL;
| ^~~~
aligner.cpp:1502:24: warning: unused variable 'alfile' [-Wunused-variable]
1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL;
| ^~~~~~
aligner.cpp:1502:40: warning: unused variable 'unfile' [-Wunused-variable]
1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL;
| ^~~~~~
aligner.cpp:1505:7: warning: unused variable 'strand' [-Wunused-variable]
1505 | int strand;
| ^~~~~~
aligner.cpp:1508:9: warning: unused variable 'ratio' [-Wunused-variable]
1508 | float ratio;
| ^~~~~
aligner.cpp:1514:31: warning: unused variable 'strata' [-Wunused-variable]
1514 | bool sorted = info->sorted, strata = info->strata;
| ^~~~~~
sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)':
sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable]
97 | char * str;
| ^~~
aligner.cpp: In member function 'AlignRes Aligner::alignPairEnd(AlignInfo*, char*)':
aligner.cpp:1685:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
1685 | for (i = 0; i < res.nRead; i++) {
| ~~^~~~~~~~~~~
sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)':
sequence.cpp:238:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
238 | for (i = 0; i < numFile; i++) {
| ~~^~~~~~~~~
sequence.cpp:309:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
309 | ( i = 0; i < nSeq; i++)
| ~~^~~~~~
sequence.cpp:324:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
324 | for (i = 0; i < numFile; i++) {
| ~~^~~~~~~~~
aligner.cpp:1754:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
1754 | delete writer;
| ^~~~~~~~~~~~~
aligner.cpp:1637:8: warning: unused variable 'success' [-Wunused-variable]
1637 | bool success;
| ^~~~~~~
aligner.cpp:1638:16: warning: unused variable 'nSuccessRead' [-Wunused-variable]
1638 | unsigned int nSuccessRead = 0;
| ^~~~~~~~~~~~
sequence.cpp:344:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
344 | for (j = 0; j < numError + 1; j++) {
| ~~^~~~~~~~~~~~~~
aligner.cpp:1639:10: warning: unused variable 'file' [-Wunused-variable]
1639 | FILE * file = NULL;
| ^~~~
aligner.cpp:1646:8: warning: unused variable 'mateFilename' [-Wunused-variable]
1646 | char mateFilename[256];
| ^~~~~~~~~~~~
aligner.cpp:1652:31: warning: unused variable 'strata' [-Wunused-variable]
1652 | bool sorted = info->sorted, strata = info->strata;
| ^~~~~~
sequence.cpp:410:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
410 | if (lenSegmentN > numError + 1) {
| ~~~~~~~~~~~~^~~~~~~~~~~~~~
sequence.cpp:429:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
429 | if (lenSegmentN > numError + 1) {
| ~~~~~~~~~~~~^~~~~~~~~~~~~~
sequence.cpp:223:16: warning: unused variable 'step' [-Wunused-variable]
223 | unsigned int step, nextstep;
| ^~~~
sequence.cpp:223:22: warning: unused variable 'nextstep' [-Wunused-variable]
223 | unsigned int step, nextstep;
| ^~~~~~~~
aligner.cpp: In member function 'AlignRes Aligner::mergeSingleEnd(AlignInfo*, int, char*)':
aligner.cpp:1851:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
1851 | delete writer;
| ^~~~~~~~~~~~~
aligner.cpp:1775:10: warning: unused variable 'ret' [-Wunused-variable]
1775 | int i, ret;
| ^~~
sequence.cpp: In member function 'int CompactSequence::filter(Aligner*, char**, int, char*)':
sequence.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
534 | for (i = 0; i < numFile; i++) {
| ~~^~~~~~~~~
sequence.cpp:599:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
599 | if (lenSegmentN > nError + 1)
| ~~~~~~~~~~~~^~~~~~~~~~~~
sequence.cpp:520:16: warning: unused variable 'step' [-Wunused-variable]
520 | unsigned int step, nextstep;
| ^~~~
sequence.cpp:520:22: warning: unused variable 'nextstep' [-Wunused-variable]
520 | unsigned int step, nextstep;
| ^~~~~~~~
sequence.cpp:521:9: warning: unused variable 'numFileChar' [-Wunused-variable]
521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment;
| ^~~~~~~~~~~
sequence.cpp:521:22: warning: unused variable 'numFileNSeg' [-Wunused-variable]
521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment;
| ^~~~~~~~~~~
sequence.cpp:521:35: warning: unused variable 'numFileSeq' [-Wunused-variable]
521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment;
| ^~~~~~~~~~
sequence.cpp:521:47: warning: unused variable 'nChar' [-Wunused-variable]
521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment;
| ^~~~~
sequence.cpp:521:54: warning: unused variable 'nNSegment' [-Wunused-variable]
521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment;
| ^~~~~~~~~
aligner.cpp: In member function 'AlignRes Aligner::mergePairEnd(AlignInfo*, int, char*)':
aligner.cpp:1989:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
1989 | delete writer;
| ^~~~~~~~~~~~~
sequence.cpp: In member function 'int CompactSequence::save(char*)':
sequence.cpp:738:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
738 | if (ret != size) {
| ~~~~^~~~~~~
aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable]
1874 | int i, ret;
| ^~~
sequence.cpp: In member function 'int CompactSequence::load(char*)':
sequence.cpp:804:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
804 | if (ret != size) {
| ~~~~^~~~~~~
hash.cpp: In member function 'int HashTable::preProcessEnd()':
hash.cpp:236:11: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32' {aka 'const unsigned int'} [-Wsign-compare]
236 | if (h >= nHistogram)
| ~~^~~~~~~~~~~~~
hash.cpp:285:33: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare]
285 | if (useEmbedTables() && tmp > embedShreshold) {
| ~~~~^~~~~~~~~~~~~~~~
hash.cpp: In member function 'void HashTable::setScanThreshold(double)':
hash.cpp:343:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
343 | for (int i = 0; i < nHistogram - 1; i++) {
| ~~^~~~~~~~~~~~~~~~
hash.cpp: In member function 'void HashTable::insert(int64*, unsigned int)':
hash.cpp:460:38: warning: operation on '*(((HashTable*)this)->HashTable::overflowPool + ((sizetype)(curOverflowEntry * 4)))' may be undefined [-Wsequence-point]
460 | overflowPool[curOverflowEntry] =
hash.cpp:411:10: warning: unused variable 'seqOffset' [-Wunused-variable]
411 | uint32 seqOffset;
| ^~~~~~~~~
hash.cpp:413:10: warning: unused variable 'counter' [-Wunused-variable]
413 | uint32 counter = 0;
| ^~~~~~~
hash.cpp:414:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable]
414 | int64 * seqVector;
| ^~~~~~~~~
hash.cpp:416:11: warning: unused variable 'target' [-Wunused-variable]
416 | int64 * target = &tspace[8];
| ^~~~~~
hash.cpp:417:8: warning: unused variable 'isBloomFilter' [-Wunused-variable]
417 | bool isBloomFilter;
| ^~~~~~~~~~~~~
hash.cpp:418:12: warning: unused variable 'bloomFilter' [-Wunused-variable]
418 | uint32 * bloomFilter;
| ^~~~~~~~~~~
hash.cpp:419:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable]
419 | uint32 bloomFilterNum;
| ^~~~~~~~~~~~~~
hash.cpp: In member function 'int HashTable::buildEmbedTable()':
hash.cpp:469:33: warning: unused variable 'rest' [-Wunused-variable]
469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40],
| ^~~~
hash.cpp:469:55: warning: unused variable 'rest1' [-Wunused-variable]
469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40],
| ^~~~~
hash.cpp:470:8: warning: unused variable 'rest2' [-Wunused-variable]
470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72];
| ^~~~~
hash.cpp:470:31: warning: unused variable 'noheadkey' [-Wunused-variable]
470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72];
| ^~~~~~~~~
hash.cpp:472:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable]
472 | uint32 seqOffset, entryOffset, startOffset;
| ^~~~~~~~~~~
hash.cpp: In member function 'void HashTable::preinsertEmbedTableEntry(int64*, int, int)':
hash.cpp:587:11: warning: unused variable 'noheadkey' [-Wunused-variable]
587 | int64 * noheadkey = &tspace[8], *rest = &tspace[24];
| ^~~~~~~~~
hash.cpp:590:8: warning: unused variable 'subkey4' [-Wunused-variable]
590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104];
| ^~~~~~~
hash.cpp:590:32: warning: unused variable 'subkey5' [-Wunused-variable]
590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104];
| ^~~~~~~
hash.cpp: In member function 'void HashTable::insertEmbedTableEntry(int64*, uint32, int, int)':
hash.cpp:662:11: warning: unused variable 'noheadkey' [-Wunused-variable]
662 | int64 * noheadkey = &tspace[8], *rest = &tspace[24];
| ^~~~~~~~~
hash.cpp:665:8: warning: unused variable 'subkey4' [-Wunused-variable]
665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104];
| ^~~~~~~
hash.cpp:665:32: warning: unused variable 'subkey5' [-Wunused-variable]
665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104];
| ^~~~~~~
hash.cpp: In member function 'unsigned int HashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)':
hash.cpp:746:7: warning: unused variable 'num' [-Wunused-variable]
746 | int num;
| ^~~
hash.cpp:750:11: warning: unused variable 'diff' [-Wunused-variable]
750 | int64 * diff = &tspace1[8], *target = &tspace2[8];
| ^~~~
hash.cpp:753:10: warning: unused variable 'sid' [-Wunused-variable]
753 | uint32 sid, soffset;
| ^~~
hash.cpp:753:15: warning: unused variable 'soffset' [-Wunused-variable]
753 | uint32 sid, soffset;
| ^~~~~~~
hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)':
hash.cpp:962:11: warning: unused variable 'noheadkey' [-Wunused-variable]
962 | int64 * noheadkey = &tspace[8], *rest = &tspace[24];
| ^~~~~~~~~
hash.cpp:965:8: warning: unused variable 'subkey4' [-Wunused-variable]
965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104];
| ^~~~~~~
hash.cpp:965:32: warning: unused variable 'subkey5' [-Wunused-variable]
965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104];
| ^~~~~~~
hash.cpp:973:11: warning: unused variable 'seqVector' [-Wunused-variable]
973 | int64 * seqVector = sequence->getSequence();
| ^~~~~~~~~
hash.cpp: In member function 'bool HashTable::lookup(int64*, uint32)':
hash.cpp:1052:7: warning: unused variable 'num' [-Wunused-variable]
1052 | int num;
| ^~~
hash.cpp:1056:11: warning: unused variable 'diff' [-Wunused-variable]
1056 | int64 * diff = &tspace1[8], *target = &tspace2[8];
| ^~~~
hash.cpp:1056:32: warning: unused variable 'target' [-Wunused-variable]
1056 | int64 * diff = &tspace1[8], *target = &tspace2[8];
| ^~~~~~
hash.cpp:1057:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable]
1057 | int64 * seqVector;
| ^~~~~~~~~
hash.cpp:1059:10: warning: unused variable 'sid' [-Wunused-variable]
1059 | uint32 sid, soffset;
| ^~~
hash.cpp:1059:15: warning: unused variable 'soffset' [-Wunused-variable]
1059 | uint32 sid, soffset;
| ^~~~~~~
hash.cpp: In member function 'uint32 HashTable::printOverflowList(uint32, uint32, int64*)':
hash.cpp:1184:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
1184 | for (int i = 0; i < keyOffset / BITS_PER_BASE; i++)
hash.cpp:1188:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
1188 | for (int i = 0; i < (lenSeq - keyOffset - lenKey) / BITS_PER_BASE; i++)
hash.cpp:1247:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
1247 | for (int j = 0; j < strlen(set[i].str); j++)
| ~~^~~~~~~~~~~~~~~~~~~~
hash.cpp:1254:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
1254 | for (int j = 0; j < strlen(set[i].str); j++)
| ~~^~~~~~~~~~~~~~~~~~~~
hash.cpp:1137:11: warning: unused variable 'diff' [-Wunused-variable]
1137 | int64 * diff = &tspace1[8], *target = &tspace2[8];
| ^~~~
hash.cpp: In member function 'int HashTable::sortList()':
hash.cpp:1430:14: warning: variable 'pool' set but not used [-Wunused-but-set-variable]
1430 | uint32 * pool;
| ^~~~
hash.cpp:1321:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable]
1321 | uint32 entryOffset, seqOffset, offset;
| ^~~~~~
hash.cpp: In member function 'void HashTable::checkRepeat(uint32)':
hash.cpp:1673:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable]
1673 | uint32 entryOffset, seqOffset, offset;
| ^~~~~~
hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label]
1690 | restart: if (buckets[bucketId] == HASH_EMPTY
| ^~~~~~~
In file included from hitset.h:31,
from writer.h:26,
from writer.cpp:21:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
writer.cpp: In member function 'void SimpleWriter::writeField(int64*, int64*, strand)':
writer.cpp:154:27: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
154 | j = BITS_PER_LONGWORD - (length * BITS_PER_BASE) & BITS_LONGWORD_MASK;
writer.cpp:148:10: warning: unused variable 'sid' [-Wunused-variable]
148 | uint32 sid = 0, soffset = 0;
| ^~~
writer.cpp:148:19: warning: unused variable 'soffset' [-Wunused-variable]
148 | uint32 sid = 0, soffset = 0;
| ^~~~~~~
writer.cpp: In member function 'void SamWriter::writeValidAlignment(int, HitSet*)':
writer.cpp:271:7: warning: unused variable 'i' [-Wunused-variable]
271 | int i, j, k, h, lastDiff;
| ^
writer.cpp:271:10: warning: unused variable 'j' [-Wunused-variable]
271 | int i, j, k, h, lastDiff;
| ^
writer.cpp:271:13: warning: unused variable 'k' [-Wunused-variable]
271 | int i, j, k, h, lastDiff;
| ^
writer.cpp:271:19: warning: unused variable 'lastDiff' [-Wunused-variable]
271 | int i, j, k, h, lastDiff;
| ^~~~~~~~
writer.cpp:272:9: warning: unused variable 'code1' [-Wunused-variable]
272 | int64 code1, code2;
| ^~~~~
writer.cpp:272:16: warning: unused variable 'code2' [-Wunused-variable]
272 | int64 code1, code2;
| ^~~~~
writer.cpp:278:10: warning: unused variable 'p' [-Wunused-variable]
278 | double p, sump;
| ^
writer.cpp:278:13: warning: unused variable 'sump' [-Wunused-variable]
278 | double p, sump;
| ^~~~
writer.cpp:279:30: warning: unused variable 'tag' [-Wunused-variable]
279 | char qseq[128], rseq[128], tag[128];
| ^~~
writer.cpp:281:8: warning: unused variable 'shortread' [-Wunused-variable]
281 | char shortread[256];
| ^~~~~~~~~
writer.cpp: In member function 'void SamWriter::getCIGAR(char*, char*, char*, ErrorVector)':
writer.cpp:382:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
382 | for (i = 0, j = 0; i < strlen(query); i++, j++) {
| ~~^~~~~~~~~~~~~~~
writer.cpp: In member function 'void SamWriter::getMDfield(char*, char*, char*, ErrorVector)':
writer.cpp:431:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
431 | for (i = 0, j = 0; i < strlen(query); i++, j++) {
| ~~^~~~~~~~~~~~~~~
writer.cpp: In member function 'void SamPairWriter::writeValidAlignment(int, HitSet*)':
writer.cpp:619:47: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
619 | if (!mate1Unmatch && !mate2Unmatch & sid1 == sid2) {
| ~~~~~^~~~~~~
In file included from embedhash.cpp:32:
edit_distance.h: At global scope:
edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable]
25 | static score_mat obj_score_mat = { 1, 1, 1, 1 };
| ^~~~~~~~~~~~~
In file included from main.cpp:38:
edit_distance.h: At global scope:
edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable]
25 | static score_mat obj_score_mat = { 1, 1, 1, 1 };
| ^~~~~~~~~~~~~
hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)':
hash.cpp:1049:1: warning: control reaches end of non-void function [-Wreturn-type]
1049 | }
| ^
In file included from hash.cpp:31:
edit_distance.h: At global scope:
edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable]
25 | static score_mat obj_score_mat = { 1, 1, 1, 1 };
| ^~~~~~~~~~~~~
In file included from hitset.h:31,
from hash.h:29,
from aligner.h:25,
from builder.cpp:31:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
682 | register unsigned long long P, M, X, U, Y;
| ^
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
hash.h: In function 'uint32 murmurHash(int64*, uint32)':
hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable]
86 | uint32 sum = 0;
| ^~~
main.cpp: In function 'void mergeFiles(std::string)':
main.cpp:269:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=]
269 | sprintf(buf, ".t%d ", i);
| ^~
main.cpp:269:18: note: directive argument in the range [0, 2147483646]
269 | sprintf(buf, ".t%d ", i);
| ^~~~~~~
main.cpp:269:12: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10
269 | sprintf(buf, ".t%d ", i);
| ~~~~~~~^~~~~~~~~~~~~~~~~
main.cpp:276:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=]
276 | sprintf(buf, ".t%d", i);
| ^~
main.cpp:276:18: note: directive argument in the range [0, 2147483646]
276 | sprintf(buf, ".t%d", i);
| ^~~~~~
main.cpp:276:12: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10
276 | sprintf(buf, ".t%d", i);
| ~~~~~~~^~~~~~~~~~~~~~~~
builder.cpp: In function 'int getArguVal(char*)':
builder.cpp:115:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
115 | else if (*c = 'g' || *c == 'G')
| ~~~^~~~~~~~~~~~~~~~~~
builder.cpp: In function 'int main(int, char**)':
builder.cpp:159:7: warning: unused variable 'build_mode' [-Wunused-variable]
159 | int build_mode = BUILD_MODE_ALL;
| ^~~~~~~~~~
builder.cpp:277:7: warning: unused variable 'nChar' [-Wunused-variable]
277 | int nChar = sequence->getNum();
| ^~~~~
sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)':
sequence.cpp:430:27: warning: 'offsetInOrgSeq' may be used uninitialized [-Wmaybe-uninitialized]
430 | offsetInOrgSeq++;
| ~~~~~~~~~~~~~~^~
sequence.cpp:221:33: note: 'offsetInOrgSeq' was declared here
221 | unsigned int offsetInCmptSeq, offsetInOrgSeq;
| ^~~~~~~~~~~~~~
In file included from builder.cpp:34:
edit_distance.h: At global scope:
edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable]
25 | static score_mat obj_score_mat = { 1, 1, 1, 1 };
| ^~~~~~~~~~~~~
sequence.cpp: In static member function 'static void CompactSequence::compose(char*, int, int64*)':
sequence.cpp:676:20: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized]
676 | forward_word = (forward_word << BITS_PER_BASE) | code;
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence.cpp:630:23: note: 'code' was declared here
630 | int64 forward_word, code;
| ^~~~
In member function 'void HashTable::setLookupInfo(int, int*)',
inlined from 'int Aligner::initLookupArray()' at aligner.cpp:375:32:
hash.h:353:18: warning: 'keySpan' may be used uninitialized [-Wmaybe-uninitialized]
353 | widthKeySpan = keySpan;
| ~~~~~~~~~~~~~^~~~~~~~~
aligner.cpp: In member function 'int Aligner::initLookupArray()':
aligner.cpp:360:7: note: 'keySpan' was declared here
360 | int keySpan;
| ^~~~~~~
aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)':
aligner.cpp:1097:3: warning: 'ret' may be used uninitialized [-Wmaybe-uninitialized]
1097 | if (ret == MSG_HITSETFULL)
| ^~
aligner.cpp:1040:7: note: 'ret' was declared here
1040 | int ret;
| ^~~
g++ -o wham sequence.o hash.o embedhash.o main.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread
g++ -o wham-build sequence.o hash.o embedhash.o builder.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread
make[1]: Leaving directory '/build/reproducible-path/wham-align-0.1.5'
dh_auto_test
rm -fr -- /tmp/dh-xdg-rundir-ukuUtazi
create-stamp debian/debhelper-build-stamp
dh_prep
rm -f -- debian/wham-align.substvars
rm -fr -- debian/.debhelper/generated/wham-align/ debian/wham-align/ debian/tmp/
dh_auto_install --destdir=debian/wham-align/
install -m0755 -d /build/reproducible-path/wham-align-0.1.5/debian/wham-align
dh_install
install -m0755 -d debian/wham-align/usr/bin
cp --reflink=auto -a ./wham ./wham-build debian/wham-align/usr/bin/
dh_installdocs
install -m0755 -d debian/wham-align/usr/share/doc/wham-align
install -m0755 -d debian/wham-align/usr/share/doc/wham-align
cp --reflink=auto -a ./MANUAL debian/wham-align/usr/share/doc/wham-align
cd './reads/..' && find 'reads' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/wham-align-0.1.5/debian/wham-align/usr/share/doc/wham-align
cd './sequences/..' && find 'sequences' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/wham-align-0.1.5/debian/wham-align/usr/share/doc/wham-align
cp --reflink=auto -a ./debian/README.test debian/wham-align/usr/share/doc/wham-align
cp --reflink=auto -a ./debian/tests/ref/README.test_data debian/wham-align/usr/share/doc/wham-align
chmod -R u\+rw,go=rX debian/wham-align/usr/share/doc
install -p -m0644 debian/copyright debian/wham-align/usr/share/doc/wham-align/copyright
install -m0755 -d debian/wham-align/usr/share/doc-base/
install -p -m0644 debian/wham-align.doc-base debian/wham-align/usr/share/doc-base/wham-align.wham
dh_installchangelogs
install -m0755 -d debian/wham-align/usr/share/doc/wham-align
install -p -m0644 debian/.debhelper/generated/wham-align/dh_installchangelogs.dch.trimmed debian/wham-align/usr/share/doc/wham-align/changelog.Debian
dh_installexamples
install -m0755 -d debian/wham-align/usr/share/doc/wham-align/examples
cp --reflink=auto -a ./reads debian/wham-align/usr/share/doc/wham-align/examples
cp --reflink=auto -a ./sequences debian/wham-align/usr/share/doc/wham-align/examples
cp --reflink=auto -a ./debian/tests/ref debian/wham-align/usr/share/doc/wham-align/examples
dh_installman
install -m0755 -d debian/wham-align/usr/share/man/man1/
install -p -m0644 ./debian/wham-build.1 debian/wham-align/usr/share/man/man1/wham-build.1
install -m0755 -d debian/wham-align/usr/share/man/man1/
install -p -m0644 ./debian/wham.1 debian/wham-align/usr/share/man/man1/wham.1
man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham-build.1
man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham.1
mv debian/wham-align/usr/share/man/man1/wham-build.1.dh-new debian/wham-align/usr/share/man/man1/wham-build.1
chmod 0644 -- debian/wham-align/usr/share/man/man1/wham-build.1
mv debian/wham-align/usr/share/man/man1/wham.1.dh-new debian/wham-align/usr/share/man/man1/wham.1
chmod 0644 -- debian/wham-align/usr/share/man/man1/wham.1
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
cd debian/wham-align
chmod a-x usr/share/doc/wham-align/MANUAL usr/share/doc/wham-align/changelog.Debian usr/share/doc/wham-align/sequences/chr1_100k.fa usr/share/man/man1/wham-build.1 usr/share/man/man1/wham.1
gzip -9nf usr/share/doc/wham-align/MANUAL usr/share/doc/wham-align/changelog.Debian usr/share/doc/wham-align/sequences/chr1_100k.fa usr/share/man/man1/wham-build.1 usr/share/man/man1/wham.1
cd '/build/reproducible-path/wham-align-0.1.5'
dh_fixperms
find debian/wham-align ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/wham-align/usr/share/doc -type f -a -true -a ! -regex 'debian/wham-align/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/wham-align/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/wham-align/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/wham-align -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/wham-align/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
dh_missing
dh_dwz -a
install -m0755 -d debian/wham-align/usr/lib/debug/.dwz/i386-linux-gnu
dwz -mdebian/wham-align/usr/lib/debug/.dwz/i386-linux-gnu/wham-align.debug -M/usr/lib/debug/.dwz/i386-linux-gnu/wham-align.debug -- debian/wham-align/usr/bin/wham debian/wham-align/usr/bin/wham-build
objcopy --compress-debug-sections debian/wham-align/usr/lib/debug/.dwz/i386-linux-gnu/wham-align.debug
chmod 0644 -- debian/wham-align/usr/lib/debug/.dwz/i386-linux-gnu/wham-align.debug
dh_strip -a
install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/5c
objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham-build debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/5c/6424c7c609b3ceaaad6844b5c2b556eed4798d.debug
chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/5c/6424c7c609b3ceaaad6844b5c2b556eed4798d.debug
strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham-build
objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/5c/6424c7c609b3ceaaad6844b5c2b556eed4798d.debug debian/wham-align/usr/bin/wham-build
install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/fc
objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/fc/b27070fcbdeb3c072773b515e385a80fec39ce.debug
chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/fc/b27070fcbdeb3c072773b515e385a80fec39ce.debug
strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham
objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/fc/b27070fcbdeb3c072773b515e385a80fec39ce.debug debian/wham-align/usr/bin/wham
install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/wham-align/usr/lib/debug/.dwz/i386-linux-gnu debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz
rm -fr debian/wham-align/usr/lib/debug/.dwz
rmdir -p --ignore-fail-on-non-empty debian/wham-align/usr/lib/debug
install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/share/doc
ln -s wham-align debian/.debhelper/wham-align/dbgsym-root/usr/share/doc/wham-align-dbgsym
install -m0755 -d debian/.debhelper/wham-align
dh_makeshlibs -a
rm -f debian/wham-align/DEBIAN/shlibs
dh_shlibdeps -a
install -m0755 -d debian/wham-align/DEBIAN
dpkg-shlibdeps -Tdebian/wham-align.substvars debian/wham-align/usr/bin/wham-build debian/wham-align/usr/bin/wham
dh_installdeb
install -m0755 -d debian/wham-align/DEBIAN
dh_gencontrol
install -m0755 -d debian/wham-align/DEBIAN
echo misc:Depends= >> debian/wham-align.substvars
echo misc:Pre-Depends= >> debian/wham-align.substvars
install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/DEBIAN
dpkg-gencontrol -pwham-align -ldebian/changelog -Tdebian/wham-align.substvars -cdebian/control -Pdebian/.debhelper/wham-align/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=wham-align-dbgsym "-DDepends=wham-align (= \${binary:Version})" "-DDescription=debug symbols for wham-align" "-DBuild-Ids=5c6424c7c609b3ceaaad6844b5c2b556eed4798d fcb27070fcbdeb3c072773b515e385a80fec39ce" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/DEBIAN/control
dpkg-gencontrol -pwham-align -ldebian/changelog -Tdebian/wham-align.substvars -cdebian/control -Pdebian/wham-align
chmod 0644 -- debian/wham-align/DEBIAN/control
dh_md5sums
install -m0755 -d debian/wham-align/DEBIAN
cd debian/wham-align >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/wham-align/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/DEBIAN
cd debian/.debhelper/wham-align/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/DEBIAN/md5sums
dh_builddeb
dpkg-deb --root-owner-group --build debian/.debhelper/wham-align/dbgsym-root ..
dpkg-deb --root-owner-group --build debian/wham-align ..
dpkg-deb: building package 'wham-align' in '../wham-align_0.1.5-8_i386.deb'.
dpkg-deb: building package 'wham-align-dbgsym' in '../wham-align-dbgsym_0.1.5-8_i386.deb'.
dpkg-genbuildinfo --build=binary -O../wham-align_0.1.5-8_i386.buildinfo
dpkg-genchanges --build=binary -O../wham-align_0.1.5-8_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/38356/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/38356/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/38356 and its subdirectories
I: Current time: Mon Mar 10 12:52:23 +14 2025
I: pbuilder-time-stamp: 1741560743