I: pbuilder: network access will be disabled during build I: Current time: Fri May 3 03:13:59 +14 2024 I: pbuilder-time-stamp: 1714655639 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: 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 gpgv: Signature made Fri Feb 19 07:13:34 2021 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./wham-align_0.1.5-8.dsc: no acceptable signature found 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/8474/tmp/hooks/D01_modify_environment starting debug: Running on ff4a. 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 May 2 13:14 /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/8474/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/8474/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]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=ddf8382f99d34a3e96e036693567e1f0 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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=8474 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.hoLgcR7T/pbuilderrc_CzpO --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.hoLgcR7T/b2 --logfile b2/build.log wham-align_0.1.5-8.dsc' SUDO_GID=113 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 2 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/8474/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: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-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 ... 19444 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} libsub-override-perl{a} libtool{a} libuchardet0{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 18.4 MB of archives. After unpacking 68.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40-8 [85.6 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-1+b1 [183 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b3 [598 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Fetched 18.4 MB in 1s (12.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19444 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_armhf.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-3_armhf.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_armhf.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.0-3_armhf.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... 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%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... 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 libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-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 .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../22-libelf1t64_0.191-1+b1_armhf.deb ... Unpacking libelf1t64:armhf (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../24-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... 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_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:armhf (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:armhf (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.37-18) ... 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/8474/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/8474/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 dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_auto_clean make -j4 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 -j4 "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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings sequence.cpp 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; | ^~~ 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)); | ~~~~~~~^~~~~~~~~~ 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; | ^~~ 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 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; | ^~~ 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 pair.h:26: rdtsc.h: In function 'long long unsigned int curtick()': rdtsc.h:32:10: warning: 'tick' is used uninitialized [-Wuninitialized] 32 | return tick; | ^~~~ rdtsc.h:20:22: note: 'tick' was declared here 20 | unsigned long long tick; | ^~~~ 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') | ~~~^~~~~~~~~~~~~~~~~~ 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; | ^ main.cpp: In function 'int main(int, char**)': main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] 523 | int numKeys; | ^~~~~~~ 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; | ^~~~~~~~ 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) { | ~~~~^~~~~~~~ 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; | ^~~ sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)': sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable] 97 | char * str; | ^~~ 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++) { | ~~^~~~~~~~~ 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++) { | ~~^~~~~~~~~~~~~~ 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; | ^~~~~~~~ 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; | ^~~~~~~~~ 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) { | ~~~~^~~~~~~ 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) { | ~~~~^~~~~~~ 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; | ^~~ 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; | ^~~~~~~~~~~~~~ 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; | ^~~ 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]; | ^~~~ embedhash.cpp:392:10: warning: unused variable 'sid' [-Wunused-variable] 392 | uint32 sid, soffset; | ^~~ embedhash.cpp:392:15: warning: unused variable 'soffset' [-Wunused-variable] 392 | uint32 sid, soffset; | ^~~~~~~ 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 }; | ^~~~~~~~~~~~~ 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); | ~~~~~~~^~~~~~~~~~~~~~~~ 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 pair.h:26: rdtsc.h: In function 'long long unsigned int curtick()': rdtsc.h:32:10: warning: 'tick' is used uninitialized [-Wuninitialized] 32 | return tick; | ^~~~ rdtsc.h:20:22: note: 'tick' was declared here 20 | unsigned long long tick; | ^~~~ 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; | ^~~~~~~~~~~~~~ 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; | ^~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings interval.cpp 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 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) { | ~~~~^~~~~~~~ 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; | ^ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings edit_distance.cpp 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; | ^~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings error.cpp 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) { | ~~~~^~~~ 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++) { | ~~^~~~~~~~~~~~ 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++) { | ~~^~~~~~~~~~~~ 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); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 += | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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++) { | ~~^~~~~~~~~~~~ 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; | ^~~~ 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; | ^~~~ 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; | ^~~ 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__; | ^~~~~~ 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++) { | ~~^~~~~~~~~~~~ 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++) { | ~~^~~~~~~~~~~ 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; | ^~~~~~ 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++) { | ~~^~~~~~~~~~~ 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; | ^~~~~~~~~~~~ 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; | ^~~~~~ 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; | ^~~ 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; | ^~~~~~~~~~~~~ aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable] 1874 | int i, ret; | ^~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings short.cpp 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; | ^~ 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) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hitset.cpp 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; | ^~~~ 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 -fstack-clash-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings model.cpp 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; | ^~~~~~~~~ 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; | ^~~~~~~ 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; | ^~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings writer.cpp 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; | ^~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings builder.cpp 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 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; | ^~~ 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(); | ^~~~~ 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 }; | ^~~~~~~~~~~~~ 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-lyVHfzn0 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/arm-linux-gnueabihf dwz -mdebian/wham-align/usr/lib/debug/.dwz/arm-linux-gnueabihf/wham-align.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/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/arm-linux-gnueabihf/wham-align.debug chmod 0644 -- debian/wham-align/usr/lib/debug/.dwz/arm-linux-gnueabihf/wham-align.debug dh_strip -a install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/ed objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/ed/ee901557deb3b0586aeffbc3fdea531e3a2367.debug chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/ed/ee901557deb3b0586aeffbc3fdea531e3a2367.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/ed/ee901557deb3b0586aeffbc3fdea531e3a2367.debug debian/wham-align/usr/bin/wham install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/fb 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/fb/f6b5862d65e43d2e5be99a514d9e909dab6666.debug chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/fb/f6b5862d65e43d2e5be99a514d9e909dab6666.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/fb/f6b5862d65e43d2e5be99a514d9e909dab6666.debug debian/wham-align/usr/bin/wham-build install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/wham-align/usr/lib/debug/.dwz/arm-linux-gnueabihf 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 debian/wham-align/usr/bin/wham-build 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=edee901557deb3b0586aeffbc3fdea531e3a2367 fbf6b5862d65e43d2e5be99a514d9e909dab6666" -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/wham-align .. dpkg-deb --root-owner-group --build debian/.debhelper/wham-align/dbgsym-root .. dpkg-deb: building package 'wham-align' in '../wham-align_0.1.5-8_armhf.deb'. dpkg-deb: building package 'wham-align-dbgsym' in '../wham-align-dbgsym_0.1.5-8_armhf.deb'. dpkg-genbuildinfo --build=binary -O../wham-align_0.1.5-8_armhf.buildinfo dpkg-genchanges --build=binary -O../wham-align_0.1.5-8_armhf.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/8474/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/8474/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/8474 and its subdirectories I: Current time: Fri May 3 03:16:23 +14 2024 I: pbuilder-time-stamp: 1714655783