bwa →
0.7.17-5+b1 →
armhf → 2020-05-28 23:33:48
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| bwa 0.7.17-5+b1 (armhf) Thu, 28 May 2020 23:26:30 +0000 |
+==============================================================================+
Package: bwa
Version: 0.7.17-5+b1
Source Version: 0.7.17-5
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-dbb2e266-0ba1-45ef-9eff-0cd14d74dfd6' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.5 MB in 24s (1015 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/bwa.git
Please use:
git clone https://salsa.debian.org/med-team/bwa.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 280 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main bwa 0.7.17-5 (dsc) [2134 B]
Get:2 http://172.17.0.1/private bullseye-staging/main bwa 0.7.17-5 (tar) [233 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main bwa 0.7.17-5 (diff) [45.0 kB]
Fetched 280 kB in 0s (1430 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bwa-WsVWfi/bwa-0.7.17' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bwa-WsVWfi' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-YHvjXF/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-YHvjXF/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-YHvjXF/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-YHvjXF/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-YHvjXF/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-YHvjXF/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-YHvjXF/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-YHvjXF/apt_archive ./ Packages [430 B]
Fetched 2106 B in 1s (2781 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 20 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-YHvjXF/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (22.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12274 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), zlib1g-dev
Filtered Build-Depends: debhelper-compat (= 12), zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-bwa-dummy' in '/<<BUILDDIR>>/resolver-YHvjXF/apt_archive/sbuild-build-depends-bwa-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-bwa-dummy sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-YHvjXF/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-YHvjXF/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-YHvjXF/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-YHvjXF/apt_archive ./ Sources [498 B]
Get:5 copy:/<<BUILDDIR>>/resolver-YHvjXF/apt_archive ./ Packages [576 B]
Fetched 2407 B in 1s (3039 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install bwa build dependencies (apt-based resolver)
---------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
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
libicu63 libmagic-mgc libmagic1 libpipeline1 libsigsegv2
libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4 man-db
po-debconf sensible-utils zlib1g-dev
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
libicu63 libmagic-mgc libmagic1 libpipeline1 libsigsegv2
libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4 man-db
po-debconf sbuild-build-depends-bwa-dummy sensible-utils zlib1g-dev
0 upgraded, 37 newly installed, 0 to remove and 20 not upgraded.
Need to get 18.9 MB of archives.
After this operation, 68.3 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-YHvjXF/apt_archive ./ sbuild-build-depends-bwa-dummy 0.invalid.0 [864 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.2-1 [318 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.1-1 [1262 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-1 [775 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.1 [187 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.8.1-1 [25.2 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.8.1-1 [14.9 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.2-1 [1158 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-3 [7987 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5 [592 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.1 [1012 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libbsd0:armhf.
(Reading database ... 12274 files and directories currently installed.)
Preparing to unpack .../00-libbsd0_0.10.0-1_armhf.deb ...
Unpacking libbsd0:armhf (0.10.0-1) ...
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Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up libmagic-mgc (1:5.38-5) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.64.2-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.1) ...
Setting up libmagic1:armhf (1:5.38-5) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-5) ...
Setting up libicu63:armhf (63.2-3) ...
Setting up autotools-dev (20180224.1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.2-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.10+dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (1.8.1-1) ...
Setting up libtool (2.4.6-14) ...
Setting up m4 (1.4.18-4) ...
Setting up bsdmainutils (11.1.2) ...
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 libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.8.1-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up automake (1:1.16.2-1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up man-db (2.9.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.1) ...
Setting up sbuild-build-depends-bwa-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.30-8+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34-8+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-12+rpi1 gcc-9_9.3.0-12+rpi1 libc6-dev_2.30-8+rpi1 libstdc++-9-dev_9.3.0-12+rpi1 libstdc++6_10.1.0-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.1.4 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8+rpi1 binutils-arm-linux-gnueabihf_2.34-8+rpi1 binutils-common_2.34-8+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.35.1-5 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-12+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.1-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.1-5 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-12+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-1+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1 gcc-8-base_8.4.0-3+rpi1 gcc-9_9.3.0-12+rpi1 gcc-9-base_9.3.0-12+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-8 libapt-pkg6.0_2.1.4 libarchive-zip-perl_1.68-1 libasan5_9.3.0-12+rpi1 libassuan0_2.5.3-7 libatomic1_10.1.0-1+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-8+rpi1 libblkid1_2.35.1-5 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-8+rpi1 libc-dev-bin_2.30-8+rpi1 libc6_2.30-8+rpi1 libc6-dev_2.30-8+rpi1 libcap-ng0_0.7.9-2.1+b1 libcap2_1:2.34-2 libcap2-bin_1:2.34-2 libcc1-0_10.1.0-1+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-8+rpi1 libctf0_2.34-8+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.252 libdebhelper-perl_13.1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.1-5 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.1-1 libgcc-9-dev_9.3.0-12+rpi1 libgcc-s1_10.1.0-1+rpi1 libgcc1_1:10.1.0-1+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10.1.0-1+rpi1 libgpg-error0_1.37-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.1-5 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.20-1 libpam-cap_1:2.34-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.1-5 libsqlite3-0_3.31.1-5 libss2_1.45.6-1 libstdc++-9-dev_9.3.0-12+rpi1 libstdc++6_10.1.0-1+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.5-3+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo5_6.2-1 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-1+rpi1 libuchardet0_0.0.6-3 libudev1_245.5-3+rpi1 libunistring2_0.9.10-2 libuuid1_2.35.1-5 libxml2_2.9.10+dfsg-5 libzstd1_1.4.4+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.35.1-5 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.30_5.30.0-10 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-bwa-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.35.1-5 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Apr 18 16:28:43 2020 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./bwa_0.7.17-5.dsc
dpkg-source: info: extracting bwa in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking bwa_0.7.17.orig.tar.gz
dpkg-source: info: unpacking bwa_0.7.17-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_heap_block_overrun
dpkg-source: info: applying fix_build_on_freebsd.patch
dpkg-source: info: applying CVE-2019-10269.patch
dpkg-source: info: applying simde
dpkg-source: info: applying spelling
dpkg-source: info: applying gcc10.patch
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 0.7.17-5+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-dbb2e266-0ba1-45ef-9eff-0cd14d74dfd6
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package bwa
dpkg-buildpackage: info: source version 0.7.17-5+b1
dpkg-buildpackage: info: source distribution bullseye-staging
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 '/<<PKGBUILDDIR>>'
rm -f gmon.out *.o a.out bwa *~ *.a
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- CFLAGS="-Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now" DFLAGS="-DHAVE_PTHREAD"
make -j4 "INSTALL=install --strip-program=true" "CFLAGS=-Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now" DFLAGS=-DHAVE_PTHREAD
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD utils.c -o utils.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD kthread.c -o kthread.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD kstring.c -o kstring.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD ksw.c -o ksw.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwt.c -o bwt.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bntseq.c -o bntseq.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwa.c -o bwa.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwamem.c -o bwamem.o
bwamem.c: In function 'mem_align1_core':
bwamem.c:1075:19: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1075 | err_printf("* %ld chains remain after removing duplicated chains\n", regs.n);
| ~~^ ~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwamem_pair.c -o bwamem_pair.o
bwamem_pair.c: In function 'mem_pestat':
bwamem_pair.c:65:99: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
| ~~^ ~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
bwamem_pair.c:65:104: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
| ~~^ ~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
bwamem_pair.c:65:109: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
| ~~^ ~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
bwamem_pair.c:65:114: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
| ~~^ ~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwamem_extra.c -o bwamem_extra.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD malloc_wrap.c -o malloc_wrap.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function 'BWTIncBuildRelativeRank':
bwt_gen.c:879:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
879 | bgint_t oldInverseSa0RelativeRank = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
bwt_gen.c: In function 'BWTIncMergeBwt':
bwt_gen.c:953:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
953 | unsigned int bitsInWordMinusBitPerChar;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD rope.c -o rope.o
rope.c: In function 'rope_restore_node':
rope.c:282:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
282 | fread(&is_bottom, 1, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
rope.c:283:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
283 | fread(&n, 2, 1, fp);
| ^~~~~~~~~~~~~~~~~~~
rope.c:291:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
291 | fread(p[i].c, 8, 6, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~
rope.c:292:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
292 | fread(q, 2, 1, fp);
| ^~~~~~~~~~~~~~~~~~
rope.c:293:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
293 | fread(q + 1, 1, *q, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~
rope.c: In function 'rope_restore':
rope.c:312:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
312 | fread(&r->max_nodes, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rope.c:313:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
313 | fread(&r->block_len, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD rle.c -o rle.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD is.c -o is.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwashm.c -o bwashm.o
bwashm.c: In function 'bwa_shm_stage':
bwashm.c:29:2: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result]
29 | ftruncate(shmid, BWA_CTL_SIZE);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bwashm.c:66:2: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result]
66 | ftruncate(shmid, idx->l_mem);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwase.c -o bwase.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bamlite.c -o bamlite.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwape.c -o bwape.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD kopen.c -o kopen.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD pemerge.c -o pemerge.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD maxk.c -o maxk.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD fastmap.c -o fastmap.o
fastmap.c: In function 'main_fastmap':
fastmap.c:413:25: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
413 | err_printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l);
| ~~^ ~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_pair.c -o bwtsw2_pair.o
gcc -c -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD main.c -o main.o
ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
ar: `u' modifier ignored since `D' is the default (see `U')
gcc -Wall -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
dh_testroot -a
dh_prep -a
dh_auto_install -a
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \
done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installchangelogs NEWS.md
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/bwa/usr/bin/bwa was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'bwa' in '../bwa_0.7.17-5+b1_armhf.deb'.
dpkg-deb: building package 'bwa-dbgsym' in '../bwa-dbgsym_0.7.17-5+b1_armhf.deb'.
dpkg-deb: building package 'libbwa-dev' in '../libbwa-dev_0.7.17-5+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../bwa_0.7.17-5+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-05-28T23:33:41Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
bwa_0.7.17-5+b1_armhf.changes:
------------------------------
Format: 1.8
Date: Sat, 18 Apr 2020 20:22:35 +0530
Source: bwa (0.7.17-5)
Binary: bwa bwa-dbgsym libbwa-dev
Binary-Only: yes
Architecture: armhf
Version: 0.7.17-5+b1
Distribution: bullseye-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
bwa - Burrows-Wheeler Aligner
libbwa-dev - Burrows-Wheeler Aligner source files
Changes:
bwa (0.7.17-5+b1) bullseye-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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26da5499314b7bacf45c59602d123d6364215deb 5147 bwa_0.7.17-5+b1_armhf.buildinfo
a528d7919c43ce91ba9ffb4bd983d98b19e45d5a 199548 bwa_0.7.17-5+b1_armhf.deb
90cd5cda8a6db34755cedfecd84d5a727cf96f1c 137824 libbwa-dev_0.7.17-5+b1_armhf.deb
Checksums-Sha256:
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Files:
bedb0875daa8c4e25eed2adf313ee575 442456 debug optional bwa-dbgsym_0.7.17-5+b1_armhf.deb
932a01f5d8a57feb709acf2f0aec600e 5147 science optional bwa_0.7.17-5+b1_armhf.buildinfo
217d2647200d74725249538b171e11da 199548 science optional bwa_0.7.17-5+b1_armhf.deb
6ba5ad10f445d24463db43fcb60c5563 137824 libdevel optional libbwa-dev_0.7.17-5+b1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
bwa-dbgsym_0.7.17-5+b1_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 442456 bytes: control archive=540 bytes.
373 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: bwa-dbgsym
Source: bwa (0.7.17-5)
Version: 0.7.17-5+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 466
Depends: bwa (= 0.7.17-5+b1)
Section: debug
Priority: optional
Description: debug symbols for bwa
Build-Ids: 97549098ed30c576808ea15036fb58ea0f6b7e61
drwxr-xr-x root/root 0 2020-04-18 14:52 ./
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/lib/
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/lib/debug/.build-id/97/
-rw-r--r-- root/root 466064 2020-04-18 14:52 ./usr/lib/debug/.build-id/97/549098ed30c576808ea15036fb58ea0f6b7e61.debug
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/share/
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-04-18 14:52 ./usr/share/doc/bwa-dbgsym -> bwa
bwa_0.7.17-5+b1_armhf.deb
-------------------------
new Debian package, version 2.0.
size 199548 bytes: control archive=1352 bytes.
1003 bytes, 22 lines control
1061 bytes, 16 lines md5sums
Package: bwa
Source: bwa (0.7.17-5)
Version: 0.7.17-5+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 431
Depends: libc6 (>= 2.29), zlib1g (>= 1:1.1.4), perl:any
Suggests: samtools
Section: science
Priority: optional
Homepage: http://bio-bwa.sourceforge.net/
Description: Burrows-Wheeler Aligner
BWA is a software package for mapping low-divergent sequences against
a large reference genome, such as the human genome. It consists of
three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first
algorithm is designed for Illumina sequence reads up to 100bp, while
the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM
and BWA-SW share similar features such as long-read support and split
alignment, but BWA-MEM, which is the latest, is generally recommended
for high-quality queries as it is faster and more accurate. BWA-MEM
also has better performance than BWA-backtrack for 70-100bp Illumina
reads.
drwxr-xr-x root/root 0 2020-04-18 14:52 ./
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/bin/
-rwxr-xr-x root/root 374744 2020-04-18 14:52 ./usr/bin/bwa
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/share/
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/share/bash-completion/
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/share/bash-completion/completions/
-rw-r--r-- root/root 384 2020-04-18 14:52 ./usr/share/bash-completion/completions/bwa
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/share/bwa/
-rwxr-xr-x root/root 613 2020-04-18 14:52 ./usr/share/bwa/qualfa2fq.pl
-rwxr-xr-x root/root 727 2020-04-18 14:52 ./usr/share/bwa/xa2multi.pl
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/share/doc/bwa/
-rw-r--r-- root/root 225 2020-04-18 14:52 ./usr/share/doc/bwa/NEWS.Debian.gz
-rw-r--r-- root/root 4216 2017-10-23 17:10 ./usr/share/doc/bwa/README-alt.md.gz
-rw-r--r-- root/root 3511 2017-10-23 17:10 ./usr/share/doc/bwa/README.md.gz
-rw-r--r-- root/root 220 2020-04-18 14:52 ./usr/share/doc/bwa/changelog.Debian.armhf.gz
-rw-r--r-- root/root 3634 2020-04-18 14:52 ./usr/share/doc/bwa/changelog.Debian.gz
-rw-r--r-- root/root 14186 2020-04-18 14:52 ./usr/share/doc/bwa/changelog.gz
-rw-r--r-- root/root 4497 2020-04-18 14:52 ./usr/share/doc/bwa/copyright
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/share/doc/bwa/examples/
-rw-r--r-- root/root 96 2020-04-18 14:52 ./usr/share/doc/bwa/examples/read1.fq
-rw-r--r-- root/root 96 2020-04-18 14:52 ./usr/share/doc/bwa/examples/read2.fq
-rw-r--r-- root/root 384 2020-04-18 14:52 ./usr/share/doc/bwa/examples/reads.fq
-rw-r--r-- root/root 192 2020-04-18 14:52 ./usr/share/doc/bwa/examples/ref.fa
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/share/man/
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/share/man/man1/
-rw-r--r-- root/root 10609 2020-04-18 14:52 ./usr/share/man/man1/bwa.1.gz
libbwa-dev_0.7.17-5+b1_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 137824 bytes: control archive=1312 bytes.
1038 bytes, 23 lines control
951 bytes, 15 lines md5sums
Package: libbwa-dev
Source: bwa (0.7.17-5)
Version: 0.7.17-5+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 356
Suggests: samtools
Section: libdevel
Priority: optional
Homepage: http://bio-bwa.sourceforge.net/
Description: Burrows-Wheeler Aligner source files
BWA is a software package for mapping low-divergent sequences against
a large reference genome, such as the human genome. It consists of
three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first
algorithm is designed for Illumina sequence reads up to 100bp, while
the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM
and BWA-SW share similar features such as long-read support and split
alignment, but BWA-MEM, which is the latest, is generally recommended
for high-quality queries as it is faster and more accurate. BWA-MEM
also has better performance than BWA-backtrack for 70-100bp Illumina
reads.
.
This package contains the source files for use in other programs.
drwxr-xr-x root/root 0 2020-04-18 14:52 ./
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/include/
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/include/bwa/
-rw-r--r-- root/root 1646 2017-10-23 17:10 ./usr/include/bwa/QSufSort.h
-rw-r--r-- root/root 2775 2017-10-23 17:10 ./usr/include/bwa/bntseq.h
-rw-r--r-- root/root 2044 2017-10-23 17:10 ./usr/include/bwa/bwa.h
-rw-r--r-- root/root 7996 2020-04-18 14:52 ./usr/include/bwa/bwamem.h
-rw-r--r-- root/root 4966 2017-10-23 17:10 ./usr/include/bwa/bwt.h
-rw-r--r-- root/root 8857 2017-10-23 17:10 ./usr/include/bwa/kseq.h
-rw-r--r-- root/root 9718 2017-10-23 17:10 ./usr/include/bwa/ksort.h
-rw-r--r-- root/root 2940 2017-10-23 17:10 ./usr/include/bwa/kvec.h
-rw-r--r-- root/root 3821 2017-10-23 17:10 ./usr/include/bwa/utils.h
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/lib/
-rw-r--r-- root/root 282528 2020-04-18 14:52 ./usr/lib/libbwa.a
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/share/
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-04-18 14:52 ./usr/share/doc/libbwa-dev/
-rw-r--r-- root/root 225 2020-04-18 14:52 ./usr/share/doc/libbwa-dev/NEWS.Debian.gz
-rw-r--r-- root/root 220 2020-04-18 14:52 ./usr/share/doc/libbwa-dev/changelog.Debian.armhf.gz
-rw-r--r-- root/root 3634 2020-04-18 14:52 ./usr/share/doc/libbwa-dev/changelog.Debian.gz
-rw-r--r-- root/root 14186 2020-04-18 14:52 ./usr/share/doc/libbwa-dev/changelog.gz
-rw-r--r-- root/root 4497 2020-04-18 14:52 ./usr/share/doc/libbwa-dev/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 8616
Build-Time: 87
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 297
Job: bwa_0.7.17-5
Machine Architecture: armhf
Package: bwa
Package-Time: 431
Source-Version: 0.7.17-5
Space: 8616
Status: successful
Version: 0.7.17-5+b1
--------------------------------------------------------------------------------
Finished at 2020-05-28T23:33:41Z
Build needed 00:07:11, 8616k disc space