samtools-legacy →
0.1.19-3 →
armhf → 2018-07-08 17:18:46
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| samtools-legacy 0.1.19-3 (armhf) Sun, 08 Jul 2018 17:14:46 +0000 |
+==============================================================================+
Package: samtools-legacy
Version: 0.1.19-3
Source Version: 0.1.19-3
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-9bc9b2c8-11c0-4cdf-873f-6e12bbb90094' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.9 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.6 MB]
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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: 'samtools-legacy' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/samtools-legacy.git
Please use:
git clone https://salsa.debian.org/med-team/samtools-legacy.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 568 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main samtools-legacy 0.1.19-3 (dsc) [2025 B]
Get:2 http://172.17.0.1/private buster-staging/main samtools-legacy 0.1.19-3 (tar) [558 kB]
Get:3 http://172.17.0.1/private buster-staging/main samtools-legacy 0.1.19-3 (diff) [8088 B]
Fetched 568 kB in 16s (36.5 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/samtools-legacy-MBzdJn/samtools-legacy-0.1.19' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/samtools-legacy-MBzdJn' 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-QsDEJb/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-QsDEJb/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-QsDEJb/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-QsDEJb/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-QsDEJb/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-QsDEJb/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-QsDEJb/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-QsDEJb/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (4122 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:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
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 37 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-QsDEJb/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
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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 (>= 11~), libncurses5-dev, zlib1g-dev
Filtered Build-Depends: debhelper (>= 11~), libncurses5-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-samtools-legacy-dummy' in '/<<BUILDDIR>>/resolver-QsDEJb/apt_archive/sbuild-build-depends-samtools-legacy-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-samtools-legacy-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-QsDEJb/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-QsDEJb/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-QsDEJb/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-QsDEJb/apt_archive ./ Sources [514 B]
Get:5 copy:/<<BUILDDIR>>/resolver-QsDEJb/apt_archive ./ Packages [593 B]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install samtools-legacy 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:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
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 libelf1
libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3
libharfbuzz0b libicu-le-hb0 libicu60 libmagic-mgc libmagic1 libncurses-dev
libncurses5-dev libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4
man-db po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
ncurses-doc 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 libelf1
libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3
libharfbuzz0b libicu-le-hb0 libicu60 libmagic-mgc libmagic1 libncurses-dev
libncurses5-dev libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4
man-db po-debconf sbuild-build-depends-samtools-legacy-dummy zlib1g-dev
0 upgraded, 39 newly installed, 0 to remove and 37 not upgraded.
Need to get 9536 kB/21.3 MB of archives.
After this operation, 70.7 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-QsDEJb/apt_archive ./ sbuild-build-depends-samtools-legacy-dummy 0.invalid.0 [880 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-3 [234 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-3 [106 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-3 [64.7 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.042-1 [20.1 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.042-1 [12.1 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.8.1-1+rpi1 [828 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.5 [981 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20180210-4 [278 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20180210-4 [936 B]
Get:32 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
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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 libncurses-dev:armhf (6.1+20180210-4) ...
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Setting up libfile-stripnondeterminism-perl (0.042-1) ...
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Setting up autoconf (2.69-11) ...
Setting up file (1:5.33-3) ...
Setting up libncurses5-dev:armhf (6.1+20180210-4) ...
Setting up automake (1:1.15.1-3.1) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2.1) ...
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Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
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Setting up gettext (0.19.8.1-6) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
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Setting up debhelper (11.3.5) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-samtools-legacy-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.30-21+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-19 gcc-7_7.3.0-19 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-8+rpi1 linux-libc-dev_4.16.12-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3 binutils_2.30-21+rpi1 binutils-arm-linux-gnueabihf_2.30-21+rpi1 binutils-common_2.30-21+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.3.0-3+rpi1 cpp-7_7.3.0-19 dash_0.5.8-2.10 dbus_1.12.8-3 dbus-user-session_1.12.8-3 debconf_1.5.67 debhelper_11.3.5 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dirmngr_2.2.8-1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.2-1 e2fsprogs_1.44.2-1 e2fsprogs-l10n_1.44.2-1 fakeroot_1.22-2 fdisk_2.32-0.1 file_1:5.33-3 findutils_4.6.0+git+20171230-2 g++_4:7.3.0-3+rpi1 g++-7_7.3.0-19 gcc_4:7.3.0-3+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b7 gcc-5-base_5.5.0-8 gcc-7_7.3.0-19 gcc-7-base_7.3.0-19 gcc-8-base_8.1.0-8+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gnupg_2.2.8-1 gnupg-agent_2.2.8-1 gnupg-l10n_2.2.8-1 gnupg-utils_2.2.8-1 gpg_2.2.8-1 gpg-agent_2.2.8-1 gpg-wks-client_2.2.8-1 gpg-wks-server_2.2.8-1 gpgconf_2.2.8-1 gpgsm_2.2.8-1 gpgv_2.2.8-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-19 libassuan0_2.5.1-2 libatomic1_8.1.0-8+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.30-21+rpi1 libblkid1_2.32-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-8+rpi1 libcilkrts5_7.3.0-19 libcom-err2_1.44.2-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.8-3 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.5-3 libext2fs2_1.44.2-1 libfakeroot_1.22-2 libfdisk1_2.32-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfreetype6_2.8.1-2 libgcc-7-dev_7.3.0-19 libgcc1_1:8.1.0-8+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8.1.0-8+rpi1 libgpg-error0_1.31-1 libgraphite2-3_1.3.11-2 libharfbuzz0b_1.8.1-1+rpi1 libhogweed4_3.4-1 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl19_0.19-1 libjson-c3_0.12.1-1.3 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-3 libmagic1_1:5.33-3 libmount1_2.32-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses-dev_6.1+20180210-4 libncurses5_6.1+20180210-4 libncurses5-dev_6.1+20180210-4 libncurses6_6.1+20180210-4 libncursesw5_6.1+20180210-4 libncursesw6_6.1+20180210-4 libnettle6_3.4-1 libnpth0_1.5-4 libnss-systemd_238-4 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-4 libpam0g_1.1.8-3.7 libpcre3_2:8.39-9 libperl5.24_5.24.1-7 libperl5.26_5.26.2-6 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-1 libprocps7_2:3.3.15-2 libreadline7_7.0-5 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-2 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32-0.1 libsqlite3-0_3.24.0-1 libss2_1.44.2-1 libssl1.1_1.1.0h-4 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-8+rpi1 libsystemd0_238-4 libtasn1-6_4.13-3 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-4 libtinfo6_6.1+20180210-4 libtool_2.4.6-2.1 libubsan0_7.3.0-19 libudev1_238-4 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32-0.1 libxml2_2.9.4+dfsg1-7 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.12-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mount_2.32-0.1 multiarch-support_2.27-3+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180210-4 ncurses-bin_6.1+20180210-4 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-6 perl-base_5.26.2-6 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-6 pinentry-curses_1.1.0-1 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-legacy-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-4 systemd-sysv_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_238-4 util-linux_2.32-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Jul 3 12:25:22 2018 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 ./samtools-legacy_0.1.19-3.dsc
dpkg-source: info: extracting samtools-legacy in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking samtools-legacy_0.1.19.orig.tar.gz
dpkg-source: info: unpacking samtools-legacy_0.1.19-3.debian.tar.xz
dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
Check disk 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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-9bc9b2c8-11c0-4cdf-873f-6e12bbb90094
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package samtools-legacy
dpkg-buildpackage: info: source version 0.1.19-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build samtools-legacy-0.1.19
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
make[2]: Leaving directory '/<<PKGBUILDDIR>>/bcftools'
make[2]: Entering directory '/<<PKGBUILDDIR>>/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
make[2]: Leaving directory '/<<PKGBUILDDIR>>/misc'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-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 -- all all-recur razip lib
make -j4 "INSTALL=install --strip-program=true" all all-recur razip lib
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
make[3]: Entering directory '/<<PKGBUILDDIR>>'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
bgzf.c: In function 'worker_aux':
bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
int i, tmp, stop = 0;
^~~
bgzf.c: In function 'bgzf_close':
bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int ret, count, block_length;
^~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
bam2bcf_indel.c: In function 'bcf_call_add_rg':
bam2bcf_indel.c:32:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
^~~
bam2bcf_indel.c:32:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
^~
bam2bcf_indel.c:33:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q;
^~~
bam2bcf_indel.c:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q;
^~
bam2bcf.c: In function 'bcf_call2bcf':
bam2bcf.c:428:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (bc->read_pos_bias != -1 )
^~
bam2bcf.c:430:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
kputc('\0', &s);
^~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
bam_import.c: In function 'append_text':
bam_import.c:179:55: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=]
fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
~~^
%d
bam_import.c:186:46: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t {aka unsigned int}' [-Wformat=]
fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,(long)header->n_text,x,y);
~~^ ~~~~~~~~~~~~~~~~~~~~~~~
%d
bam_import.c:186:58: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t {aka unsigned int}' [-Wformat=]
fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,(long)header->n_text,x,y);
~~^
%d
bam_import.c:186:64: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t {aka unsigned int}' [-Wformat=]
fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,(long)header->n_text,x,y);
~~^
%d
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
errmod.c: In function 'errmod_cal':
errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare]
if (m > m) return -1;
^
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l;
^~~~~~~
cut_target.c: In function 'process_cns.isra.1':
cut_target.c:96:2: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
for (i = 0, s = -1; i <= l; ++i) {
^~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
bam2depth.c: In function 'main_depth':
bam2depth.c:85:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
bam2depth.c:87:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
data = calloc(n, sizeof(void*)); // data[i] for the i-th input
^~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
padding.c: In function 'bam_pad2unpad':
padding.c:173:88: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t {aka unsigned int}' [-Wformat=]
fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
~~^ ~~~
%d
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
bam_pileup.c: In function 'resolve_cigar2':
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
int k, is_head = 0;
^~~~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
faidx.c: In function 'fai_load':
faidx.c:277:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
faidx.c:280:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
if (fp == 0) {
^~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
faidx.c: In function 'fai_load':
faidx.c:277:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
faidx.c:280:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
if (fp == 0) {
^~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
bam_reheader.c: In function 'bam_reheader':
bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
bam_header_t *old;
^~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
^~~~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>/bcftools'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
bcf.c: In function 'bcf_fmt_core':
bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
int iPL = -1;
^~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
bcfutils.c: In function 'bcf_fit_alt':
bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
int ipl=-1, igt=-1;
^~~
bcfutils.c: In function 'bcf_fix_gt':
bcfutils.c:254:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
bcfutils.c:256:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':';
^
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[4]: Entering directory '/<<PKGBUILDDIR>>/bcftools'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
bcfutils.c: In function 'bcf_fit_alt':
bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
int ipl=-1, igt=-1;
^~~
bcfutils.c: In function 'bcf_fix_gt':
bcfutils.c:254:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
else
^~~~
bcfutils.c:256:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':';
^
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
int i, n, n2;
^~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -g -Wall -O2 -o razip razip.o razf.o knetfile.o -lz
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
ar: `u' modifier ignored since `D' is the default (see `U')
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[3]: Leaving directory '/<<PKGBUILDDIR>>/bcftools'
make[3]: Entering directory '/<<PKGBUILDDIR>>/misc'
make[3]: Nothing to be done for 'lib'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/misc'
gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Leaving directory '/<<PKGBUILDDIR>>/bcftools'
make[4]: Entering directory '/<<PKGBUILDDIR>>/misc'
make[4]: Nothing to be done for 'lib'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/misc'
gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>/bcftools'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
call1.c: In function 'write_header':
call1.c:303:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (!strstr(str.s, "##FORMAT=<ID=GL,"))
^~
call1.c:305:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (!strstr(str.s, "##FORMAT=<ID=DP,"))
^~
gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
make[3]: Leaving directory '/<<PKGBUILDDIR>>/bcftools'
make[3]: Entering directory '/<<PKGBUILDDIR>>/misc'
gcc -c -g -Wall -O2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
gcc -g -Wall -O2 -c -I.. -o md5fa.o md5fa.c
gcc -g -Wall -O2 -o maq2sam-short maq2sam.c -lz
md5.c: In function 'MD5Final':
md5.c:155:26: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess]
memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
^
md5.c: In function 'MD5Final':
md5.c:155:26: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess]
memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
^
gcc -g -Wall -O2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -g -Wall -O2 -c -I.. -o ace2sam.o ace2sam.c
gcc -g -Wall -O2 -c -I.. -o wgsim.o wgsim.c
gcc -g -Wall -O2 -c -I.. -o bamcheck.o bamcheck.c
ace2sam.c: In function 'main':
ace2sam.c:112:40: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t {aka unsigned int}' [-Wformat=]
fprintf(stderr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[is_padded?1:2].l); // The SAM header line
~~^ ~~~~~~~~~~~~~~~~~~
%d
ace2sam.c:162:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (write_cns) puts(t[4].s); t[4].l = 0;
^~
ace2sam.c:162:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if (write_cns) puts(t[4].s); t[4].l = 0;
^
gcc -g -Wall -O2 -o md5sum-lite md5sum-lite.o
gcc -g -Wall -O2 -o md5fa md5.o md5fa.o -lz
gcc -g -Wall -O2 -o wgsim wgsim.o -lm -lz
gcc -g -Wall -O2 -o ace2sam ace2sam.o -lz
gcc -g -Wall -O2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
make[3]: Leaving directory '/<<PKGBUILDDIR>>/misc'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/make -C examples all
make[2]: Entering directory '/<<PKGBUILDDIR>>/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
../samtools index ex1.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
[samopen] SAM header is present: 2 sequences.
(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
../samtools rmdup ex1f.bam ex1f-rmduppe.bam
[bam_rmdup_core] processing reference seq1...
[bam_rmdup_core] processing reference seq2...
[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/examples'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
dh_install -a
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installchangelogs NEWS
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'libbam-dev' in '../libbam-dev_0.1.19-3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../samtools-legacy_0.1.19-3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build samtools-legacy-0.1.19
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-07-08T17:18:40Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
samtools-legacy_0.1.19-3_armhf.changes:
---------------------------------------
Format: 1.8
Date: Tue, 03 Jul 2018 14:19:56 +0200
Source: samtools-legacy
Binary: libbam-dev
Architecture: armhf
Version: 0.1.19-3
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
Changes:
samtools-legacy (0.1.19-3) unstable; urgency=medium
.
* Team upload.
* Switch from cdbs to dh
* Add watch file
* Cleanup debian/upstream/metadata
* cme fix dpkg-control
- Point VCS fields to Salsa
- Standards-Version: 4.1.4
- Fix spacing in short description
* debhelper 11
* Fix Homepage
* Remove redundant information debian/reference
Checksums-Sha1:
32a74e688d913a300b95dda91386a11e95f0d723 104860 libbam-dev_0.1.19-3_armhf.deb
d122a1830a3e58bcec3fcbe648f31cb7a6fe8ee2 4495 samtools-legacy_0.1.19-3_armhf.buildinfo
Checksums-Sha256:
ad3b4bdc1cdcaebf983e4059b9a42f11c7267fe4f36ddda67b7af3d7e7e369a1 104860 libbam-dev_0.1.19-3_armhf.deb
30b5ee1480c290fed084162cd5283a497d8f80925f3673b1d3c16a8027140c80 4495 samtools-legacy_0.1.19-3_armhf.buildinfo
Files:
9d815932978b66f7c080d5b71d75f2ff 104860 libdevel optional libbam-dev_0.1.19-3_armhf.deb
2dfeb9ab3a1a6ad936eab59643d707d6 4495 science optional samtools-legacy_0.1.19-3_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libbam-dev_0.1.19-3_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 104860 bytes: control archive=1088 bytes.
853 bytes, 19 lines control
654 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools-legacy
Version: 0.1.19-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 308
Section: libdevel
Priority: optional
Homepage: http://www.htslib.org/
Description: manipulates nucleotide sequence alignments in BAM or SAM format
The BAM library provides I/O and various operations on manipulating nucleotide
sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
Alignment/Map) format. It now supports importing from or exporting to SAM,
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
.
This library is part of SAMtools version 0.1.19. It is obsolete and provided
only to build software that has not yet transitioned to the HTSlib, which
replaces this library.
drwxr-xr-x root/root 0 2018-07-03 12:19 ./
drwxr-xr-x root/root 0 2018-07-03 12:19 ./usr/
drwxr-xr-x root/root 0 2018-07-03 12:19 ./usr/include/
drwxr-xr-x root/root 0 2018-07-03 12:19 ./usr/include/samtools/
-rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
-rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
-rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
drwxr-xr-x root/root 0 2018-07-03 12:19 ./usr/lib/
-rw-r--r-- root/root 225346 2018-07-03 12:19 ./usr/lib/libbam.a
drwxr-xr-x root/root 0 2018-07-03 12:19 ./usr/share/
drwxr-xr-x root/root 0 2018-07-03 12:19 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-07-03 12:19 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 381 2018-07-03 12:19 ./usr/share/doc/libbam-dev/README.Debian
-rw-r--r-- root/root 2699 2018-07-03 12:19 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
-rw-r--r-- root/root 5038 2018-07-03 12:19 ./usr/share/doc/libbam-dev/copyright
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 9848
Build-Time: 45
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 149
Job: samtools-legacy_0.1.19-3
Machine Architecture: armhf
Package: samtools-legacy
Package-Time: 234
Source-Version: 0.1.19-3
Space: 9848
Status: successful
Version: 0.1.19-3
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Finished at 2018-07-08T17:18:40Z
Build needed 00:03:54, 9848k disk space