bwa →
0.7.17-6 →
armhf → 2021-02-07 06:12:48
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| bwa 0.7.17-6 (armhf) Sun, 07 Feb 2021 06:06:33 +0000 |
+==============================================================================+
Package: bwa
Version: 0.7.17-6
Source Version: 0.7.17-6
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-9823d873-605a-4e4b-a05a-a34fdd422411' 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 [12.2 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.2 MB]
Fetched 25.3 MB in 28s (897 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 245 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main bwa 0.7.17-6 (dsc) [2116 B]
Get:2 http://172.17.0.1/private bullseye-staging/main bwa 0.7.17-6 (tar) [233 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main bwa 0.7.17-6 (diff) [10.7 kB]
Fetched 245 kB in 0s (841 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bwa-fEMpg4/bwa-0.7.17' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bwa-fEMpg4' 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-a8Pmw5/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-a8Pmw5/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-a8Pmw5/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-a8Pmw5/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-a8Pmw5/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-a8Pmw5/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-a8Pmw5/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-a8Pmw5/apt_archive ./ Packages [434 B]
Fetched 2110 B in 1s (2909 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:
bsdextrautils krb5-locales libnss-nis libnss-nisplus netbase sensible-utils
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 14 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-a8Pmw5/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (22.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12526 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 (= 13), zlib1g-dev, libsimde-dev
Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libsimde-dev
dpkg-deb: building package 'sbuild-build-depends-bwa-dummy' in '/<<BUILDDIR>>/resolver-a8Pmw5/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-a8Pmw5/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-a8Pmw5/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-a8Pmw5/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-a8Pmw5/apt_archive ./ Sources [504 B]
Get:5 copy:/<<BUILDDIR>>/resolver-a8Pmw5/apt_archive ./ Packages [587 B]
Fetched 2424 B in 1s (3311 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:
krb5-locales libnss-nis libnss-nisplus netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libicu67 libmagic-mgc libmagic1
libpipeline1 libsigsegv2 libsimde-dev libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc 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 libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libicu67 libmagic-mgc libmagic1
libpipeline1 libsigsegv2 libsimde-dev libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-bwa-dummy
zlib1g-dev
0 upgraded, 32 newly installed, 0 to remove and 14 not upgraded.
Need to get 17.7 MB of archives.
After this operation, 69.3 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-a8Pmw5/apt_archive ./ sbuild-build-depends-bwa-dummy 0.invalid.0 [872 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-3 [170 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-3 [32.4 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-3 [509 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.3 [189 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.10.0-1 [25.6 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.10.0-1 [15.3 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-3 [162 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20210126-1 [163 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-6 [8289 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-3 [1214 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.3 [1011 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libsimde-dev all 0.7.2-3 [259 kB]
Get:32 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
Fetched 17.7 MB in 5s (3364 kB/s)
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12526 files and directories currently installed.)
Preparing to unpack .../00-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
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Preparing to unpack .../01-groff-base_1.22.4-6_armhf.deb ...
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Unpacking gettext-base (0.21-3) ...
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Unpacking sbuild-build-depends-bwa-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libsimde-dev (0.7.2-3) ...
Setting up libicu67:armhf (67.1-6) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.3.3) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up gettext-base (0.21-3) ...
Setting up file (1:5.39-3) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libsigsegv2:armhf (2.12-3) ...
Setting up autopoint (0.21-3) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libelf1:armhf (0.182-3) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.3) ...
Setting up libfile-stripnondeterminism-perl (1.10.0-1) ...
Setting up gettext (0.21-3) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.10.0-1) ...
Setting up dwz (0.13+20210126-1) ...
Setting up groff-base (1.22.4-6) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.3.3) ...
Setting up sbuild-build-depends-bwa-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-9+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_2.35.1-7+rpi1 dpkg-dev_1.20.7.1+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-9+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.4-1+rpi1
Package versions: adduser_3.118 apt_2.1.18 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-3 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1-2 binutils_2.35.1-7+rpi1 binutils-arm-linux-gnueabihf_2.35.1-7+rpi1 binutils-common_2.35.1-7+rpi1 bsdextrautils_2.36.1-6 bsdutils_1:2.36.1-6 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.74 debhelper_13.3.3 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.10.0-1 diffutils_1:3.7-5 dirmngr_2.2.20-1 dpkg_1.20.7.1+rpi1 dpkg-dev_1.20.7.1+rpi1 dwz_0.13+20210126-1 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-6+rpi1 gettext_0.21-3 gettext-base_0.21-3 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_3.6-1 groff-base_1.22.4-6 gzip_1.10-2 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 krb5-locales_1.18.3-4 libacl1_2.2.53-9 libapt-pkg6.0_2.1.18 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.1-7+rpi1 libblkid1_2.36.1-6 libbz2-1.0_1.0.8-4 libc-bin_2.31-9+rpi1 libc-dev-bin_2.31-9+rpi1 libc6_2.31-9+rpi1 libc6-dev_2.31-9+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.45.6-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-7+rpi1 libctf0_2.35.1-7+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.256 libdebhelper-perl_13.3.3 libdpkg-perl_1.20.7.1+rpi1 libelf1_0.182-3 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1.1 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.10.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.0-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-4 libhogweed6_3.6-2 libicu67_67.1-6 libidn2-0_2.3.0-5 libisl23_0.23-1 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libksba8_1.5.0-3 libldap-2.4-2_2.4.56+dfsg-1+rpi1+b1 libldap-common_2.4.56+dfsg-1+rpi1 liblz4-1_1.9.3-1+rpi1 liblzma5_5.2.5-1.0 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-6 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-2 libnettle8_3.6-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.22-1 libpam-modules_1.4.0-2 libpam-modules-bin_1.4.0-2 libpam-runtime_1.4.0-2 libpam0g_1.4.0-2 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.0-6 libpipeline1_1.5.3-1 libreadline8_8.1-1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-2+b1 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.12-3 libsimde-dev_0.7.2-3 libsmartcols1_2.36.1-6 libsqlite3-0_3.34.1-1 libss2_1.45.6-1 libssl1.1_1.1.1i-2 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.2-5+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.2-5+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-6 libxml2_2.9.10+dfsg-6.3 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-1 linux-libc-dev_5.10.4-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36.1-6 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.2 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.0-6 perl-base_5.32.0-6 perl-modules-5.32_5.32.0-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 sbuild-build-depends-bwa-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysvinit-utils_2.96-5 tar_1.32+dfsg-1+rpi1 tzdata_2020f-1 util-linux_2.36.1-6 xz-utils_5.2.5-1.0 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 '/tmp/dpkg-verify-sig.GXl4gQVJ/trustedkeys.kbx': General error
gpgv: Signature made Thu Feb 4 15:16:58 2021 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./bwa_0.7.17-6.dsc
dpkg-source: info: extracting bwa in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking bwa_0.7.17.orig.tar.gz
dpkg-source: info: unpacking bwa_0.7.17-6.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
dpkg-source: info: applying hurd
Check disc space
----------------
Sufficient free space for build
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-9823d873-605a-4e4b-a05a-a34fdd422411
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package bwa
dpkg-buildpackage: info: source version 0.7.17-6
dpkg-buildpackage: info: source distribution unstable
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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD utils.c -o utils.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD kthread.c -o kthread.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD kstring.c -o kstring.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD ksw.c -o ksw.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwt.c -o bwt.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bntseq.c -o bntseq.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwa.c -o bwa.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwamem.c -o bwamem.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwamem_pair.c -o bwamem_pair.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
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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD rle.c -o rle.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD is.c -o is.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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:33:2: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result]
33 | ftruncate(shmid, BWA_CTL_SIZE);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bwashm.c:70:2: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result]
70 | ftruncate(shmid, idx->l_mem);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwase.c -o bwase.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bamlite.c -o bamlite.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwape.c -o bwape.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD kopen.c -o kopen.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD pemerge.c -o pemerge.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD maxk.c -o maxk.o
gcc -c -Wall -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -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_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 -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -a
dh_installdeb -a
debian/rules override_dh_gencontrol
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-3), "
dpkg-gencontrol: warning: package bwa: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package bwa: substitution variable ${perl:Depends} unused, but is defined
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'bwa' in '../bwa_0.7.17-6_armhf.deb'.
dpkg-deb: building package 'bwa-dbgsym' in '../bwa-dbgsym_0.7.17-6_armhf.deb'.
dpkg-deb: building package 'libbwa-dev' in '../libbwa-dev_0.7.17-6_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../bwa_0.7.17-6_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 2021-02-07T06:12:38Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
bwa_0.7.17-6_armhf.changes:
---------------------------
Format: 1.8
Date: Thu, 04 Feb 2021 16:16:02 +0100
Source: bwa
Binary: bwa bwa-dbgsym libbwa-dev
Architecture: armhf
Version: 0.7.17-6
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Michael R. Crusoe <crusoe@debian.org>
Description:
bwa - Burrows-Wheeler Aligner
libbwa-dev - Burrows-Wheeler Aligner source files
Changes:
bwa (0.7.17-6) unstable; urgency=medium
.
[ Michael R. Crusoe ]
* debian/patches/hurd: define PATH_MAX, if needed (fixes FTBFS on hurd-*)
* Switch to libsimde-dev from our code copy
* Build libbwa.a with -fPIC for uncalled
.
[ Andreas Tille ]
* Drop redundant debian/gbp.conf
* Demote perl from Depends to Recommends
.
[ Michael R. Crusoe ]
* Forward many patches upstream
* Standards-Version: 4.5.1 (routine-update)
* debhelper-compat 13 (routine-update)
* watch file standard 4 (routine-update)
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a9bd66efc419701f7a728f65b27a58f9abb0f13b 195368 bwa_0.7.17-6_armhf.deb
b758b31e9f348b71f2ff4530454da6314cfde511 137052 libbwa-dev_0.7.17-6_armhf.deb
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Files:
4e23307fc513fd4254098d32cc66f647 415908 debug optional bwa-dbgsym_0.7.17-6_armhf.deb
a0cf8dff06b6a701f4657b2d2798e41c 5105 science optional bwa_0.7.17-6_armhf.buildinfo
6d55a757434877f6f9bb3a7737684d21 195368 science optional bwa_0.7.17-6_armhf.deb
981d77abdd4fa87573e007a5cdb0f741 137052 libdevel optional libbwa-dev_0.7.17-6_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
bwa-dbgsym_0.7.17-6_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 415908 bytes: control archive=532 bytes.
356 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: bwa-dbgsym
Source: bwa
Version: 0.7.17-6
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 438
Depends: bwa (= 0.7.17-6)
Section: debug
Priority: optional
Description: debug symbols for bwa
Build-Ids: e31af2a92221513ac90c20681e37fa7d4c107ee2
drwxr-xr-x root/root 0 2021-02-04 15:16 ./
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/lib/
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/lib/debug/.build-id/e3/
-rw-r--r-- root/root 438228 2021-02-04 15:16 ./usr/lib/debug/.build-id/e3/1af2a92221513ac90c20681e37fa7d4c107ee2.debug
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/share/
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-02-04 15:16 ./usr/share/doc/bwa-dbgsym -> bwa
bwa_0.7.17-6_armhf.deb
----------------------
new Debian package, version 2.0.
size 195368 bytes: control archive=1332 bytes.
1015 bytes, 23 lines control
983 bytes, 15 lines md5sums
Package: bwa
Version: 0.7.17-6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 426
Depends: libc6 (>= 2.29), zlib1g (>= 1:1.1.4)
Recommends: perl
Suggests: samtools
Built-Using: simde (= 0.7.2-3)
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 2021-02-04 15:16 ./
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/bin/
-rwxr-xr-x root/root 370648 2021-02-04 15:16 ./usr/bin/bwa
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/share/
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/share/bash-completion/
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/share/bash-completion/completions/
-rw-r--r-- root/root 384 2019-12-14 10:13 ./usr/share/bash-completion/completions/bwa
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/share/bwa/
-rwxr-xr-x root/root 613 2021-02-04 15:16 ./usr/share/bwa/qualfa2fq.pl
-rwxr-xr-x root/root 727 2021-02-04 15:16 ./usr/share/bwa/xa2multi.pl
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/share/doc/bwa/
-rw-r--r-- root/root 225 2020-04-20 16:02 ./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 3817 2021-02-04 15:16 ./usr/share/doc/bwa/changelog.Debian.gz
-rw-r--r-- root/root 14186 2021-02-04 15:16 ./usr/share/doc/bwa/changelog.gz
-rw-r--r-- root/root 4397 2021-02-04 15:16 ./usr/share/doc/bwa/copyright
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/share/doc/bwa/examples/
-rw-r--r-- root/root 96 2019-12-14 10:13 ./usr/share/doc/bwa/examples/read1.fq
-rw-r--r-- root/root 96 2019-12-14 10:13 ./usr/share/doc/bwa/examples/read2.fq
-rw-r--r-- root/root 384 2019-12-14 10:13 ./usr/share/doc/bwa/examples/reads.fq
-rw-r--r-- root/root 192 2019-12-14 10:13 ./usr/share/doc/bwa/examples/ref.fa
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/share/man/
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/share/man/man1/
-rw-r--r-- root/root 10609 2021-02-04 15:16 ./usr/share/man/man1/bwa.1.gz
libbwa-dev_0.7.17-6_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 137052 bytes: control archive=1304 bytes.
1055 bytes, 24 lines control
866 bytes, 14 lines md5sums
Package: libbwa-dev
Source: bwa
Version: 0.7.17-6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 356
Suggests: samtools
Built-Using: simde (= 0.7.2-3)
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 2021-02-04 15:16 ./
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/include/
drwxr-xr-x root/root 0 2021-02-04 15:16 ./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 2021-02-04 15:16 ./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 2021-02-04 15:16 ./usr/lib/
-rw-r--r-- root/root 282820 2021-02-04 15:16 ./usr/lib/libbwa.a
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/share/
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-02-04 15:16 ./usr/share/doc/libbwa-dev/
-rw-r--r-- root/root 225 2020-04-20 16:02 ./usr/share/doc/libbwa-dev/NEWS.Debian.gz
-rw-r--r-- root/root 3817 2021-02-04 15:16 ./usr/share/doc/libbwa-dev/changelog.Debian.gz
-rw-r--r-- root/root 14186 2021-02-04 15:16 ./usr/share/doc/libbwa-dev/changelog.gz
-rw-r--r-- root/root 4397 2021-02-04 15:16 ./usr/share/doc/libbwa-dev/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 7900
Build-Time: 86
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 228
Job: bwa_0.7.17-6
Machine Architecture: armhf
Package: bwa
Package-Time: 365
Source-Version: 0.7.17-6
Space: 7900
Status: successful
Version: 0.7.17-6
--------------------------------------------------------------------------------
Finished at 2021-02-07T06:12:38Z
Build needed 00:06:05, 7900k disc space