samtools-legacy →
0.1.19+dfsg-4 →
armhf → 2021-10-05 06:31:12
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| samtools-legacy 0.1.19+dfsg-4 (armhf) Tue, 05 Oct 2021 06:25:07 +0000 |
+==============================================================================+
Package: samtools-legacy
Version: 0.1.19+dfsg-4
Source Version: 0.1.19+dfsg-4
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-e1d40639-07b7-40fb-af18-a0179011c516' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.8 MB in 27s (948 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: '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 382 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main samtools-legacy 0.1.19+dfsg-4 (dsc) [2135 B]
Get:2 http://172.17.0.1/private bookworm-staging/main samtools-legacy 0.1.19+dfsg-4 (tar) [371 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main samtools-legacy 0.1.19+dfsg-4 (diff) [8732 B]
Fetched 382 kB in 0s (1808 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/samtools-legacy-jPVckX/samtools-legacy-0.1.19+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/samtools-legacy-jPVckX' 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-Kq9XPI/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-Kq9XPI/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-Kq9XPI/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-Kq9XPI/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Kq9XPI/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Kq9XPI/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Kq9XPI/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Kq9XPI/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2600 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 22 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Kq9XPI/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 12484 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), libncurses5-dev, zlib1g-dev
Filtered Build-Depends: debhelper-compat (= 13), libncurses5-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-samtools-legacy-dummy' in '/<<BUILDDIR>>/resolver-Kq9XPI/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-Kq9XPI/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Kq9XPI/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Kq9XPI/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Kq9XPI/apt_archive ./ Sources [511 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Kq9XPI/apt_archive ./ Packages [595 B]
Fetched 2439 B in 1s (3256 B/s)
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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils 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
libncurses-dev libncurses5-dev libncurses6 libpipeline1 libsigsegv2
libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf
sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc 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 libgpm2 libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils 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
libncurses-dev libncurses5-dev libncurses6 libpipeline1 libsigsegv2
libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf
sbuild-build-depends-samtools-legacy-dummy sensible-utils zlib1g-dev
0 upgraded, 36 newly installed, 0 to remove and 22 not upgraded.
Need to get 18.1 MB of archives.
After this operation, 67.4 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Kq9XPI/apt_archive ./ sbuild-build-depends-samtools-legacy-dummy 0.invalid.0 [884 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-4 [79.7 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf libncurses-dev armhf 6.2+20201114-4 [288 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libncurses5-dev armhf 6.2+20201114-4 [940 B]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
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Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up bsdextrautils (2.37.2-1) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
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Setting up libsub-override-perl (0.09-2) ...
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Setting up libxml2:armhf (2.9.12+dfsg-5) ...
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Setting up gettext (0.21-4) ...
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Setting up automake (1:1.16.4-2) ...
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 (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up debhelper (13.5.2) ...
Setting up sbuild-build-depends-samtools-legacy-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-9+rpi1 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 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_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-4+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libasan6_11.2.0-4+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-4+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-4+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.3.0-9+rpi1 libgcc-s1_11.2.0-4+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-4+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses-dev_6.2+20201114-4 libncurses5-dev_6.2+20201114-4 libncurses6_6.2+20201114-4 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.9-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-legacy-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.37.2-1 xz-utils_5.2.5-2 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.ZFjvMdaR/trustedkeys.kbx': General error
gpgv: Signature made Fri Oct 1 15:06:37 2021 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+dfsg-4.dsc
dpkg-source: info: extracting samtools-legacy in /<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg
dpkg-source: info: unpacking samtools-legacy_0.1.19+dfsg.orig.tar.xz
dpkg-source: info: unpacking samtools-legacy_0.1.19+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
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
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying gcc-11.patch
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=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-e1d40639-07b7-40fb-af18-a0179011c516
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package samtools-legacy
dpkg-buildpackage: info: source version 0.1.19+dfsg-4
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 '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
make[2]: Entering directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
make[2]: Leaving directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
make[2]: Entering directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/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 '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/bcftools'
make[2]: Entering directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/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 '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/misc'
make[1]: Leaving directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
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 '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
dh_auto_build -- all all-recur razip lib CFLAGS="-g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2"
make -j4 "INSTALL=install --strip-program=true" all all-recur razip lib "CFLAGS=-g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2"
make[2]: Entering directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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=]
179 | fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
| ~~^ ~
| | |
| long int size_t {aka unsigned int}
| %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=]
186 | fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,(long)header->n_text,x,y);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long int uint32_t {aka unsigned int}
| %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=]
186 | fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,(long)header->n_text,x,y);
| ~~^ ~
| | |
| long int size_t {aka unsigned int}
| %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=]
186 | fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,(long)header->n_text,x,y);
| ~~^ ~
| | |
| long int size_t {aka unsigned int}
| %d
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
bam_index.c: In function 'bam_index_core':
bam_index.c:178:35: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow]
178 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
| ^~~~~~~~
bam_index.c: In function 'bam_index_load_core':
bam_index.c:335:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
335 | fread(magic, 1, 4, fp);
| ^~~~~~~~~~~~~~~~~~~~~~
bam_index.c:342:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
342 | fread(&idx->n, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~
bam_index.c:355:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
355 | fread(&size, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~
bam_index.c:358:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
358 | fread(&key, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~
bam_index.c:362:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
362 | fread(&p->n, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~
bam_index.c:366:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
366 | fread(p->list, 16, p->n, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
bam_index.c:376:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
376 | fread(&index2->n, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
bam_index.c:380:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
380 | fread(index2->offset, index2->n, 8, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
razf.c: In function 'razf_flush':
razf.c:221:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:234:4: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c: In function '_razf_write':
razf.c:201:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c: In function 'razf_close':
razf.c:804:4: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
804 | write(rz->x.fpw, &rz->in, sizeof(int64_t));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:805:4: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
805 | write(rz->x.fpw, &rz->out, sizeof(int64_t));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:808:4: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
808 | write(rz->x.fpw, &v64, sizeof(int64_t));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:810:4: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
810 | write(rz->x.fpw, &v64, sizeof(int64_t));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c: In function 'razf_end_flush':
razf.c:258:4: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c: In function 'save_zindex':
razf.c:96:12: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
96 | if(is_be) write(fd, &rz->index->size, sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:99:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
99 | write(fd, &v32, sizeof(uint32_t));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:106:2: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:107:2: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
In file included from knetfile.c:46:
knetfile.c: In function 'kftp_send_cmd':
knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
9 | #define netwrite(fd, ptr, len) write(fd, ptr, len)
| ^~~~~~~~~~~~~~~~~~~
knetfile.c:236:2: note: in expansion of macro 'netwrite'
236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
| ^~~~~~~~
knetfile.c: In function 'khttp_connect_file':
knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
9 | #define netwrite(fd, ptr, len) write(fd, ptr, len)
| ^~~~~~~~~~~~~~~~~~~
knetfile.c:415:2: note: in expansion of macro 'netwrite'
415 | netwrite(fp->fd, buf, l);
| ^~~~~~~~
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.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=]
173 | 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);
| ~~^ ~~~
| | |
| long int size_t {aka unsigned int}
| %d
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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
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 '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
make[3]: Entering directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/bcftools'
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
make[3]: Entering directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
make[4]: Entering directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
make[4]: Nothing to be done for 'lib'.
make[4]: Leaving directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
make[4]: Entering directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/bcftools'
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
make[2]: Nothing to be done for 'lib'.
razip.c: In function 'main':
razip.c:131:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
131 | write(f_dst, buffer, c);
| ^~~~~~~~~~~~~~~~~~~~~~~
razip.c: In function 'write_open':
razip.c:32:4: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result]
32 | scanf("%c", &c);
| ^~~~~~~~~~~~~~~
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/bcftools'
make[3]: Entering directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/misc'
make[3]: Nothing to be done for 'lib'.
make[3]: Leaving directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/misc'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/bcftools'
make[4]: Entering directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/misc'
make[4]: Nothing to be done for 'lib'.
make[4]: Leaving directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/misc'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
make[3]: Entering directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/bcftools'
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -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 -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
make[3]: Leaving directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/bcftools'
make[3]: Entering directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/misc'
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.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=]
112 | fprintf(stderr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[is_padded?1:2].l); // The SAM header line
| ~~^ ~~~~~~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
make[3]: Leaving directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/misc'
make[2]: Leaving directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
/usr/bin/make -C examples all
make[2]: Entering directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/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
cc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread -Wl,-z,relro
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
make[2]: Leaving directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg/examples'
make[1]: Leaving directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install --destdir=debian/libbam-dev/ -a
dh_install -a
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
dh_installchangelogs NEWS
make[1]: Leaving directory '/<<BUILDDIR>>/samtools-legacy-0.1.19+dfsg'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: Depends field of package libbam-dev: substitution variable ${shlibs:Depends} used, but is not defined
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'libbam-dev' in '../libbam-dev_0.1.19+dfsg-4_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../samtools-legacy_0.1.19+dfsg-4_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 2021-10-05T06:31:05Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
samtools-legacy_0.1.19+dfsg-4_armhf.changes:
--------------------------------------------
Format: 1.8
Date: Fri, 01 Oct 2021 17:04:40 +0200
Source: samtools-legacy
Binary: libbam-dev
Architecture: armhf
Version: 0.1.19+dfsg-4
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <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+dfsg-4) unstable; urgency=medium
.
* Team upload.
* Fix watchfile to detect new versions on github
* Standards-Version: 4.6.0 (routine-update)
* Fix error: format not a string literal and no format arguments
Checksums-Sha1:
6a38608c9540c4bf3211f68b6dc731784fa60d4e 105736 libbam-dev_0.1.19+dfsg-4_armhf.deb
c6aae7acf728e8f256ed6371aea5018317771ba8 4807 samtools-legacy_0.1.19+dfsg-4_armhf.buildinfo
Checksums-Sha256:
c491cf93ba872d4d7b7eed179528c3d88afeb64fe3efa4d636cfaa0a983bbbe4 105736 libbam-dev_0.1.19+dfsg-4_armhf.deb
2a43e18ae6444910eb1cede7a43c7e6824276f45e71287f9aaf2c899256f200c 4807 samtools-legacy_0.1.19+dfsg-4_armhf.buildinfo
Files:
3e45dd685fd938ff73cfd3087ac93bbb 105736 libdevel optional libbam-dev_0.1.19+dfsg-4_armhf.deb
72a608fc168fb7975dce9bb9613480b1 4807 science optional samtools-legacy_0.1.19+dfsg-4_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libbam-dev_0.1.19+dfsg-4_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 105736 bytes: control archive=1104 bytes.
879 bytes, 20 lines control
654 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools-legacy
Version: 0.1.19+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 302
Depends: zlib1g-dev
Section: libdevel
Priority: optional
Homepage: https://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 2021-10-01 15:04 ./
drwxr-xr-x root/root 0 2021-10-01 15:04 ./usr/
drwxr-xr-x root/root 0 2021-10-01 15:04 ./usr/include/
drwxr-xr-x root/root 0 2021-10-01 15:04 ./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 2021-10-01 15:04 ./usr/lib/
-rw-r--r-- root/root 219490 2021-10-01 15:04 ./usr/lib/libbam.a
drwxr-xr-x root/root 0 2021-10-01 15:04 ./usr/share/
drwxr-xr-x root/root 0 2021-10-01 15:04 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-01 15:04 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 381 2021-10-01 15:04 ./usr/share/doc/libbam-dev/README.Debian
-rw-r--r-- root/root 3187 2021-10-01 15:04 ./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 3824 2021-10-01 15:04 ./usr/share/doc/libbam-dev/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 10776
Build-Time: 114
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 193
Job: samtools-legacy_0.1.19+dfsg-4
Machine Architecture: armhf
Package: samtools-legacy
Package-Time: 358
Source-Version: 0.1.19+dfsg-4
Space: 10776
Status: successful
Version: 0.1.19+dfsg-4
--------------------------------------------------------------------------------
Finished at 2021-10-05T06:31:05Z
Build needed 00:05:58, 10776k disc space