https://launchpad.net/ubuntu/+source/wham-align/0.1.5-2build1/+build/19113154 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-065 5.3.0-13-generic #14+riscv64.5-Ubuntu SMP Wed Nov 13 20:10:41 UTC 2019 riscv64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu1 dpkg-dev_1.19.7ubuntu2 python-debian_0.1.36build1. Syncing the system clock with the buildd NTP service... 21 Apr 23:10:36 ntpdate[71550]: adjust time server 10.211.37.1 offset 0.000290 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19113154 --image-type chroot /home/buildd/filecache-default/af01171acfc9164a9204c952c1e623f3f59763a9 Creating target for build PACKAGEBUILD-19113154 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19113154 Starting target for build PACKAGEBUILD-19113154 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19113154 'deb http://ftpmaster.internal/ubuntu focal main universe' Overriding sources.list in build-PACKAGEBUILD-19113154 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19113154 Updating target for build PACKAGEBUILD-19113154 Ign:1 http://archive-team.internal/bootstrap/riscv64 focal InRelease Get:2 http://ftpmaster.internal/ubuntu focal InRelease [265 kB] Get:3 http://archive-team.internal/bootstrap/riscv64 focal Release [754 B] Ign:4 http://archive-team.internal/bootstrap/riscv64 focal Release.gpg Get:5 http://ftpmaster.internal/ubuntu focal-proposed InRelease [265 kB] Get:6 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 Packages [34.3 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 Packages [875 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main Translation-en [506 kB] Get:9 http://ftpmaster.internal/ubuntu focal/universe riscv64 Packages [7931 kB] Get:10 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5127 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 Packages [13.1 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [6516 B] Get:13 http://ftpmaster.internal/ubuntu focal-proposed/restricted Translation-en [496 B] Get:14 http://ftpmaster.internal/ubuntu focal-proposed/universe riscv64 Packages [137 kB] Get:15 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [82.2 kB] Get:16 http://ftpmaster.internal/ubuntu focal-proposed/multiverse riscv64 Packages [1140 B] Get:17 http://ftpmaster.internal/ubuntu focal-proposed/multiverse Translation-en [4136 B] Fetched 15.2 MB in 24s (626 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libssl1.1 openssl 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1562 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main riscv64 libssl1.1 riscv64 1.1.1f-1ubuntu2 [967 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main riscv64 openssl riscv64 1.1.1f-1ubuntu2 [595 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1562 kB in 1s (2905 kB/s) (Reading database ... 9817 files and directories currently installed.) Preparing to unpack .../libssl1.1_1.1.1f-1ubuntu2_riscv64.deb ... Unpacking libssl1.1:riscv64 (1.1.1f-1ubuntu2) over (1.1.1f-1ubuntu1) ... Preparing to unpack .../openssl_1.1.1f-1ubuntu2_riscv64.deb ... Unpacking openssl (1.1.1f-1ubuntu2) over (1.1.1f-1ubuntu1) ... Setting up libssl1.1:riscv64 (1.1.1f-1ubuntu2) ... Setting up openssl (1.1.1f-1ubuntu2) ... Processing triggers for libc-bin (2.31-0ubuntu9) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19113154 riscv64 focal -c chroot:build-PACKAGEBUILD-19113154 --arch=riscv64 --dist=focal --nolog wham-align_0.1.5-2build1.dsc Initiating build PACKAGEBUILD-19113154 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 5.3.0-13-generic #14+riscv64.5-Ubuntu SMP Wed Nov 13 20:10:41 UTC 2019 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lcy01-065 +==============================================================================+ | wham-align 0.1.5-2build1 (riscv64) Tue, 21 Apr 2020 23:12:26 +0000 | +==============================================================================+ Package: wham-align Version: 0.1.5-2build1 Source Version: 0.1.5-2build1 Distribution: focal Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19113154/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/wham-align-tNj13J/resolver-XSwG9O' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- wham-align_0.1.5-2build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/wham-align-tNj13J/wham-align-0.1.5' with '<>' I: NOTICE: Log filtering will replace 'build/wham-align-tNj13J' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 11), build-essential, fakeroot Filtered Build-Depends: debhelper (>= 11), build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [365 B] Get:5 copy:/<>/apt_archive ./ Packages [449 B] Fetched 1771 B in 0s (5358 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libgpm2 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu66 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf tzdata Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu66 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy tzdata 0 upgraded, 35 newly installed, 0 to remove and 0 not upgraded. Need to get 17.0 MB of archives. After this operation, 67.6 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [872 B] Get:2 http://ftpmaster.internal/ubuntu focal/main riscv64 libbsd0 riscv64 0.10.0-1 [42.0 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main riscv64 bsdmainutils riscv64 11.1.2ubuntu3 [176 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main riscv64 libuchardet0 riscv64 0.0.6-3build1 [64.9 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main riscv64 groff-base riscv64 1.22.4-4build1 [816 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main riscv64 libpipeline1 riscv64 1.5.2-2build1 [23.9 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 man-db riscv64 2.9.1-1 [1075 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main riscv64 libmagic-mgc riscv64 1:5.38-4 [218 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main riscv64 libmagic1 riscv64 1:5.38-4 [70.5 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main riscv64 file riscv64 1:5.38-4 [22.5 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main riscv64 libelf1 riscv64 0.176-1.1build1 [41.8 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main riscv64 libglib2.0-0 riscv64 2.64.2-1~fakesync1 [1123 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main riscv64 tzdata all 2019c-3ubuntu1 [294 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main riscv64 libicu66 riscv64 66.1-2ubuntu2 [8406 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main riscv64 libxml2 riscv64 2.9.10+dfsg-5 [559 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main riscv64 gettext-base riscv64 0.19.8.1-10build1 [47.4 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main riscv64 libsigsegv2 riscv64 2.12-2 [13.0 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main riscv64 m4 riscv64 1.4.18-4 [188 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main riscv64 autoconf all 2.69-11.1 [321 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main riscv64 autotools-dev all 20180224.1 [39.6 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main riscv64 automake all 1:1.16.1-4ubuntu6 [522 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main riscv64 autopoint all 0.19.8.1-10build1 [412 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main riscv64 libtool all 2.4.6-14 [161 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main riscv64 dh-autoreconf all 19 [16.1 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main riscv64 libdebhelper-perl all 12.10ubuntu1 [62.1 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main riscv64 libarchive-zip-perl all 1.67-2 [90.5 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main riscv64 libsub-override-perl all 0.09-2 [9532 B] Get:28 http://ftpmaster.internal/ubuntu focal/main riscv64 libfile-stripnondeterminism-perl all 1.7.0-1 [15.9 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main riscv64 dh-strip-nondeterminism all 1.7.0-1 [5228 B] Get:30 http://ftpmaster.internal/ubuntu focal/main riscv64 dwz riscv64 0.13-5 [147 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main riscv64 libcroco3 riscv64 0.6.13-1 [71.1 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main riscv64 gettext riscv64 0.19.8.1-10build1 [844 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main riscv64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main riscv64 po-debconf all 1.0.21 [233 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main riscv64 debhelper all 12.10ubuntu1 [877 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.0 MB in 3s (6097 kB/s) Selecting previously unselected package libbsd0:riscv64. (Reading database ... 9817 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_riscv64.deb ... Unpacking libbsd0:riscv64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu3_riscv64.deb ... Unpacking bsdmainutils (11.1.2ubuntu3) ... Selecting previously unselected package libuchardet0:riscv64. Preparing to unpack .../02-libuchardet0_0.0.6-3build1_riscv64.deb ... Unpacking libuchardet0:riscv64 (0.0.6-3build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-4build1_riscv64.deb ... Unpacking groff-base (1.22.4-4build1) ... Selecting previously unselected package libpipeline1:riscv64. Preparing to unpack .../04-libpipeline1_1.5.2-2build1_riscv64.deb ... Unpacking libpipeline1:riscv64 (1.5.2-2build1) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.9.1-1_riscv64.deb ... Unpacking man-db (2.9.1-1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.38-4_riscv64.deb ... Unpacking libmagic-mgc (1:5.38-4) ... Selecting previously unselected package libmagic1:riscv64. Preparing to unpack .../07-libmagic1_1%3a5.38-4_riscv64.deb ... Unpacking libmagic1:riscv64 (1:5.38-4) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.38-4_riscv64.deb ... Unpacking file (1:5.38-4) ... Selecting previously unselected package libelf1:riscv64. Preparing to unpack .../09-libelf1_0.176-1.1build1_riscv64.deb ... Unpacking libelf1:riscv64 (0.176-1.1build1) ... Selecting previously unselected package libglib2.0-0:riscv64. Preparing to unpack .../10-libglib2.0-0_2.64.2-1~fakesync1_riscv64.deb ... Unpacking libglib2.0-0:riscv64 (2.64.2-1~fakesync1) ... Selecting previously unselected package tzdata. Preparing to unpack .../11-tzdata_2019c-3ubuntu1_all.deb ... Unpacking tzdata (2019c-3ubuntu1) ... Selecting previously unselected package libicu66:riscv64. Preparing to unpack .../12-libicu66_66.1-2ubuntu2_riscv64.deb ... Unpacking libicu66:riscv64 (66.1-2ubuntu2) ... Selecting previously unselected package libxml2:riscv64. Preparing to unpack .../13-libxml2_2.9.10+dfsg-5_riscv64.deb ... Unpacking libxml2:riscv64 (2.9.10+dfsg-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../14-gettext-base_0.19.8.1-10build1_riscv64.deb ... Unpacking gettext-base (0.19.8.1-10build1) ... Selecting previously unselected package libsigsegv2:riscv64. Preparing to unpack .../15-libsigsegv2_2.12-2_riscv64.deb ... Unpacking libsigsegv2:riscv64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../16-m4_1.4.18-4_riscv64.deb ... Unpacking m4 (1.4.18-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../17-autoconf_2.69-11.1_all.deb ... Unpacking autoconf (2.69-11.1) ... 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Unpacking libcroco3:riscv64 (0.6.13-1) ... Selecting previously unselected package gettext. Preparing to unpack .../30-gettext_0.19.8.1-10build1_riscv64.deb ... Unpacking gettext (0.19.8.1-10build1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../31-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../32-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../33-debhelper_12.10ubuntu1_all.deb ... Unpacking debhelper (12.10ubuntu1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../34-sbuild-build-depends-main-dummy_0.invalid.0_riscv64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:riscv64 (1.5.2-2build1) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libarchive-zip-perl (1.67-2) ... Setting up libglib2.0-0:riscv64 (2.64.2-1~fakesync1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.10ubuntu1) ... Setting up libmagic1:riscv64 (1:5.38-4) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-4) ... Setting up tzdata (2019c-3ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Apr 21 23:14:04 UTC 2020. Universal Time is now: Tue Apr 21 23:14:04 UTC 2020. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20180224.1) ... Setting up libsigsegv2:riscv64 (2.12-2) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up libuchardet0:riscv64 (0.0.6-3build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libbsd0:riscv64 (0.10.0-1) ... Setting up libelf1:riscv64 (0.176-1.1build1) ... Setting up libfile-stripnondeterminism-perl (1.7.0-1) ... Setting up libtool (2.4.6-14) ... Setting up libicu66:riscv64 (66.1-2ubuntu2) ... Setting up m4 (1.4.18-4) ... Setting up bsdmainutils (11.1.2ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.7.0-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4build1) ... Setting up libxml2:riscv64 (2.9.10+dfsg-5) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcroco3:riscv64 (0.6.13-1) ... Setting up gettext (0.19.8.1-10build1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.10ubuntu1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu9) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.3.0-13-generic #14+riscv64.5-Ubuntu SMP Wed Nov 13 20:10:41 UTC 2019 riscv64 (riscv64) Toolchain package versions: binutils_2.34-6ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-10ubuntu2 gcc-9_9.3.0-10ubuntu2 libc6-dev_2.31-0ubuntu9 libstdc++-9-dev_9.3.0-10ubuntu2 libstdc++6_10-20200411-0ubuntu1 linux-libc-dev_5.4.0-24.28 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.0.2 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu5 base-passwd_3.5.47 bash_5.0-6ubuntu1 binutils_2.34-6ubuntu1 binutils-common_2.34-6ubuntu1 binutils-riscv64-linux-gnu_2.34-6ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.34-0.1ubuntu9 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110ubuntu1 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-10ubuntu2 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.10ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.7.0-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu3 dpkg-dev_1.19.7ubuntu3 dwz_0.13-5 e2fsprogs_1.45.5-2ubuntu1 fakeroot_1.24-1 file_1:5.38-4 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-10ubuntu2 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10-20200411-0ubuntu1 gcc-8-base_8.4.0-3ubuntu2 gcc-9_9.3.0-10ubuntu2 gcc-9-base_9.3.0-10ubuntu2 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.19-3ubuntu2 gpg-agent_2.2.19-3ubuntu2 gpgconf_2.2.19-3ubuntu2 gpgv_2.2.19-3ubuntu2 grep_3.4-1 groff-base_1.22.4-4build1 gzip_1.10-0ubuntu4 hostname_3.23 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readline-common_8.0-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1ubuntu1 tar_1.30+dfsg-7 tzdata_2019c-3ubuntu1 ubuntu-keyring_2020.02.11.2 util-linux_2.34-0.1ubuntu9 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: wham-align Binary: wham-align Architecture: any Version: 0.1.5-2build1 Maintainer: Steffen Moeller Homepage: http://research.cs.wisc.edu/wham Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/wham-align Vcs-Git: https://salsa.debian.org/med-team/wham-align.git Build-Depends: debhelper (>= 11) Package-List: wham-align deb science optional arch=any Checksums-Sha1: e1ecc46d4ab3af47518fbdee4b8efab2c7a89bb9 120296 wham-align_0.1.5.orig.tar.gz e63d98c9de3a0805e0ee6a6d04a48990196c6a67 3056 wham-align_0.1.5-2build1.debian.tar.xz Checksums-Sha256: c020b999c0d4a3a8e29b32e91dba559b6d6ce3a221081212689c9662828d7b02 120296 wham-align_0.1.5.orig.tar.gz 2189a68ddefb664be06ff83282b981f1767c7ac50b3a66584f421b9fb72b5430 3056 wham-align_0.1.5-2build1.debian.tar.xz Files: 56e14e483b0fed5ae5faa4d1621ee3d7 120296 wham-align_0.1.5.orig.tar.gz 6cefe0bffe26f133fd30da31930e98d2 3056 wham-align_0.1.5-2build1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJEBAEBCAAuFiEE1WVxuIqLuvFAv2PWvX6qYHePpvUFAl53kfEQHGRva29AdWJ1 bnR1LmNvbQAKCRC9fqpgd4+m9cJjD/47FfISWh/OnJ3tEVjpHv3uQYa1126TPVpK tjlijptC0lJ+gUr9yIbGrl9TIcGqfpqwVSkji0t0niXN30ZZBO/XXPTvrBgCP5ML LdAr9UdByFJNmzIXRxVJHQaZmfQYNKRBKBFFFrU4Fs4pILH2m20MMLnFLNjA8a6t J3tlcxO05yZ1982mkfEIOcUDJl9bCN4x5f3IHod7VGtCqLfZCziDDiWRXuKXir2Z Y2WYOj03cIvAIwfp/0jndnZcZPp0Ye5HXSlXwSGkjNlMGrGfvfTYqvp+0IxoVoQ7 R9PWWAZRIYntW3RT3n2rDDHSV/k8IZN8Z+RvH+po60BrM74asZRHFm3wVavw88qI YCfBTPC28QhpRHC88XspfnWOZYUrJsm9ye6R/KaXpr/JcQtIHz9lt+8bdJvTISl7 J1+WVMvqepbQPRTNvxZMneU/Jqd0HB78PENi8yhj9FXXjojbhZTKC4OZZ5I8G4ik vyuN3sMHpDxBLAGHi1ktul/N5/S4YAV/3feYDzncKX/s2s3BKWYU5Yp9rBq4bQHc YkH/Lf8Y/kZ+ZKTMRz/hHJs5Iq0LwIf3m7xCw/Z56SaFBWekJZf2PPqTkuFRWK68 BgAiEl/YlbeVBST5NexJsotjw/bdvgw2qtPUNRM75+5f3MVxNymnZfIAodUcIMqp OuBuut/kfg== =SgIl -----END PGP SIGNATURE----- gpgv: Signature made Sun Mar 22 16:27:29 2020 UTC gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 gpgv: issuer "doko@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./wham-align_0.1.5-2build1.dsc dpkg-source: info: extracting wham-align in /<> dpkg-source: info: unpacking wham-align_0.1.5.orig.tar.gz dpkg-source: info: unpacking wham-align_0.1.5-2build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying makefile.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=8 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19113154 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19113154 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19113154 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package wham-align dpkg-buildpackage: info: source version 0.1.5-2build1 dpkg-buildpackage: info: source distribution focal dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 fakeroot debian/rules clean dh clean dh_auto_clean make -j8 clean make[1]: Entering directory '/<>' rm -f wham wham-build *.o make[1]: Leaving directory '/<>' 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 \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j8 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' g++ -c -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -Wno-write-strings hash.cpp g++ -c -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -Wno-write-strings embedhash.cpp g++ -c -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -Wno-write-strings main.cpp g++ -c -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -Wno-write-strings sequence.cpp g++ -c -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -Wno-write-strings aligner.cpp g++ -c -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -Wno-write-strings interval.cpp g++ -c -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -Wno-write-strings edit_distance.cpp g++ -c -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -Wno-write-strings error.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__; | ^~~~~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from aligner.cpp:25: pair.h:840:2: error: #error "POPCNT is only supported in Intel X86/IA-64 architectures" 840 | #error "POPCNT is only supported in Intel X86/IA-64 architectures" | ^~~~~ In file included from hitset.h:31, from hash.h:29, from hash.cpp:27: pair.h:840:2: error: #error "POPCNT is only supported in Intel X86/IA-64 architectures" 840 | #error "POPCNT is only supported in Intel X86/IA-64 architectures" | ^~~~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from main.cpp:34: pair.h:840:2: error: #error "POPCNT is only supported in Intel X86/IA-64 architectures" 840 | #error "POPCNT is only supported in Intel X86/IA-64 architectures" | ^~~~~ In file included from hitset.h:31, from hash.h:29, from embedhash.cpp:27: pair.h:840:2: error: #error "POPCNT is only supported in Intel X86/IA-64 architectures" 840 | #error "POPCNT is only supported in Intel X86/IA-64 architectures" | ^~~~~ g++ -c -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -Wno-write-strings short.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 sequence.cpp:30: pair.h:840:2: error: #error "POPCNT is only supported in Intel X86/IA-64 architectures" 840 | #error "POPCNT is only supported in Intel X86/IA-64 architectures" | ^~~~~ 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) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 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 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::pairAlignBitVector64(int64*, int64*, int, int, int)’: 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:972:23: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 972 | 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: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:972:23: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 972 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from aligner.h:25, from aligner.cpp:25: 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 hash.cpp:27: hash.h: In function ‘uint32 murmurHash(int64*, uint32)’: hash.h:86:10: warning: unused variable ‘sum’ [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ 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: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:972:23: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 972 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from embedhash.cpp:27: 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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -Wno-write-strings hitset.cpp In file included from hitset.h:31, from hitset.cpp:1: pair.h:840:2: error: #error "POPCNT is only supported in Intel X86/IA-64 architectures" 840 | #error "POPCNT is only supported in Intel X86/IA-64 architectures" | ^~~~~ short.cpp: In member function ‘int ShortRead::load(int)’: short.cpp:422:28: warning: ‘code’ may be used uninitialized in this function [-Wmaybe-uninitialized] 422 | forward_word = ~((~code) | (-1LL << forward_offset)); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, 2147483646] 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); | ^~~~~~~~ In file included from /usr/include/stdio.h:867, from short.h:24, from short.cpp:27: /usr/include/riscv64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 4 and 268 bytes into a destination of size 256 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, 2147483646] 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ^~~~~~~~ In file included from /usr/include/stdio.h:867, from short.h:24, from short.cpp:27: /usr/include/riscv64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 4 and 268 bytes into a destination of size 256 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: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 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::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; | ^ 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; | ^~ pair.h: In static member function ‘static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)’: pair.h:972:23: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 972 | 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: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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -Wno-write-strings perfcounters.cpp pair.h: In static member function ‘static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)’: pair.h:972:23: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 972 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from aligner.h:25, from main.cpp:34: hash.h: In function ‘uint32 murmurHash(int64*, uint32)’: hash.h:86:10: warning: unused variable ‘sum’ [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ 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; | ^~~~~~~~~ make[1]: *** [makefile:58: hitset.o] Error 1 make[1]: *** Waiting for unfinished jobs.... perfcounters.cpp:27:2: error: #error Performance counters not known for this architecture. 27 | #error Performance counters not known for this architecture. | ^~~~~ perfcounters.cpp:40:2: error: #error Performance counters not known for this architecture. 40 | #error Performance counters not known for this architecture. | ^~~~~ perfcounters.cpp:81:2: error: #error Performance counters not known for this architecture. 81 | #error Performance counters not known for this architecture. | ^~~~~ make[1]: *** [makefile:76: perfcounters.o] Error 1 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) { | ~~~~^~~~~~~~~~~~~~~~ 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) { | ~~~~^~~~ 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)(((long unsigned int)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: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; | ^~~~~~~~~~~~~~ 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++) { | ~~^~~~~~~~~~~~ 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]; | ^~~~~~~~~ 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; | ^ 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]; | ^~~~~~~ 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) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]; | ^~~~~~~~~ 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); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]; | ^~~~~~~ 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 += | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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; | ^~~~~~~ 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++) { | ~~^~~~~~~~~~~~ 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(); | ^~~~~~~~~ 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; | ^~~~ 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: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 ‘long 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 ‘long 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]; | ^~~~ 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++) { | ~~^~~~~~~~~~~~ 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:1629:10: 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; | ^~~~~~ hash.cpp: In member function ‘void HashTable::checkRepeat(uint32)’: hash.cpp:1690:5: warning: label ‘restart’ defined but not used [-Wunused-label] 1690 | restart: if (buckets[bucketId] == HASH_EMPTY | ^~~~~~~ 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:1754:10: 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:1851:10: 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:1989:10: 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; | ^~~ 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; | ^~~~~~~~ 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)(((long unsigned int)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: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: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; | ^~~~~~~ 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 }; | ^~~~~~~~~~~~~ make[1]: *** [makefile:40: hash.o] Error 1 aligner.cpp: In member function ‘AlignRes Aligner::mergeSingleEnd(AlignInfo*, int, char*)’: aligner.cpp:1860:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1860 | system(command); | ~~~~~~^~~~~~~~~ aligner.cpp: In member function ‘AlignRes Aligner::mergePairEnd(AlignInfo*, int, char*)’: aligner.cpp:2002:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2002 | system(command); | ~~~~~~^~~~~~~~~ aligner.cpp:2004:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2004 | system(command); | ~~~~~~^~~~~~~~~ make[1]: *** [makefile:43: aligner.o] Error 1 main.cpp: In function ‘void mergeFiles(std::string)’: main.cpp:273:9: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 273 | system(command.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~ main.cpp:278:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 278 | system(command.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~ 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 }; | ^~~~~~~~~~~~~ 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 }; | ^~~~~~~~~~~~~ make[1]: *** [makefile:37: embedhash.o] Error 1 make[1]: *** [makefile:46: main.o] Error 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: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:972:23: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 972 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from aligner.h:25, from sequence.cpp:30: 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) { | ~~~~^~~~~~~ make[1]: *** [makefile:49: sequence.o] Error 1 make[1]: Leaving directory '/<>' dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" returned exit code 2 make: *** [debian/rules:9: build-arch] Error 25 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-04-21T23:15:02Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 1348 Build-Time: 35 Distribution: focal Fail-Stage: build Host Architecture: riscv64 Install-Time: 98 Job: wham-align_0.1.5-2build1.dsc Machine Architecture: riscv64 Package: wham-align Package-Time: 156 Source-Version: 0.1.5-2build1 Space: 1348 Status: attempted Version: 0.1.5-2build1 -------------------------------------------------------------------------------- Finished at 2020-04-21T23:15:02Z Build needed 00:02:36, 1348k disk space E: Build failure (dpkg-buildpackage died) RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19113154 Scanning for processes to kill in build PACKAGEBUILD-19113154 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19113154 Stopping target for build PACKAGEBUILD-19113154 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19113154 Removing build PACKAGEBUILD-19113154