smalt →
0.7.6-9 →
armhf → 2020-01-06 05:43:42
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| smalt 0.7.6-9 (armhf) Mon, 06 Jan 2020 05:03:17 +0000 |
+==============================================================================+
Package: smalt
Version: 0.7.6-9
Source Version: 0.7.6-9
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-83bf697a-a40f-4113-83f3-745cc7a93b0a' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.2 MB in 27s (908 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: 'smalt' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/smalt.git
Please use:
git clone https://salsa.debian.org/med-team/smalt.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 72.3 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main smalt 0.7.6-9 (dsc) [2064 B]
Get:2 http://172.17.0.1/private bullseye-staging/main smalt 0.7.6-9 (tar) [72.3 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main smalt 0.7.6-9 (diff) [8756 B]
Fetched 72.3 MB in 7s (10.4 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/smalt-9C4uyT/smalt-0.7.6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/smalt-9C4uyT' 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-WzdKie/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-WzdKie/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-WzdKie/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-WzdKie/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-WzdKie/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-WzdKie/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-WzdKie/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-WzdKie/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2852 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 30 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-WzdKie/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13002 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 all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), zlib1g-dev, python3, samtools, libbambamc-dev
Filtered Build-Depends: debhelper-compat (= 12), zlib1g-dev, python3, samtools, libbambamc-dev
dpkg-deb: building package 'sbuild-build-depends-smalt-dummy' in '/<<BUILDDIR>>/resolver-WzdKie/apt_archive/sbuild-build-depends-smalt-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-smalt-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-WzdKie/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-WzdKie/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-WzdKie/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-WzdKie/apt_archive ./ Sources [518 B]
Get:5 copy:/<<BUILDDIR>>/resolver-WzdKie/apt_archive ./ Packages [598 B]
Fetched 2449 B in 1s (3333 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install smalt build dependencies (apt-based resolver)
-----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbambamc-dev libbambamc0
libbrotli1 libbsd0 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0
libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0
libgssapi-krb5-2 libhts2 libicu63 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14
libpipeline1 libpsl5 libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib librtmp1 libsigsegv2 libssh2-1 libssl1.1
libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4 man-db
mime-support pkg-config po-debconf python3 python3-minimal python3.7
python3.7-minimal samtools sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc
krb5-user libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor
less www-browser libmail-box-perl python3-doc python3-tk python3-venv
python3.7-venv python3.7-doc binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libltdl-dev
libmail-sendmail-perl cwltool
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 libbambamc-dev libbambamc0
libbrotli1 libbsd0 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0
libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0
libgssapi-krb5-2 libhts2 libicu63 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14
libpipeline1 libpsl5 libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib librtmp1 libsigsegv2 libssh2-1 libssl1.1
libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4 man-db
mime-support pkg-config po-debconf python3 python3-minimal python3.7
python3.7-minimal samtools sbuild-build-depends-smalt-dummy sensible-utils
zlib1g-dev
0 upgraded, 66 newly installed, 0 to remove and 30 not upgraded.
Need to get 27.0 MB of archives.
After this operation, 99.7 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-WzdKie/apt_archive ./ sbuild-build-depends-smalt-dummy 0.invalid.0 [892 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-1 [29.5 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [1261 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.6-1 [585 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.6-1 [1527 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.5-3 [36.8 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.6-1 [1669 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.6-1 [350 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.5-3 [20.2 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.5-3 [62.1 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.3 [174 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-1 [23.6 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-1 [14.6 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.4-1 [1138 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.3 [1019 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libbambamc0 armhf 0.0.50-3 [30.4 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libbambamc-dev armhf 0.0.50-3 [42.6 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6 [261 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1 [73.9 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.67.0-2 [284 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.5-1 [78.0 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libhts2 armhf 1.9-12 [275 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20191019-1 [79.5 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.9-7 [399 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking gettext (0.19.8.1-10) ...
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Unpacking sbuild-build-depends-smalt-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.2-1) ...
Setting up libkeyutils1:armhf (1.6-6) ...
Setting up libpsl5:armhf (0.20.2-2) ...
Setting up mime-support (3.64) ...
Setting up libmagic-mgc (1:5.37-6) ...
Setting up libarchive-zip-perl (1.67-1) ...
Setting up libglib2.0-0:armhf (2.62.4-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (12.7.3) ...
Setting up libbrotli1:armhf (1.0.7-6) ...
Setting up libnghttp2-14:armhf (1.40.0-1) ...
Setting up libmagic1:armhf (1:5.37-6) ...
Setting up libdeflate0 (1.5-1) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.37-6) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up libkrb5support0:armhf (1.17-6+b1) ...
Setting up autotools-dev (20180224.1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libncurses6:armhf (6.1+20191019-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libbambamc0 (0.0.50-3) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up pkg-config (0.29-6) ...
Setting up libk5crypto3:armhf (1.17-6+b1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-6+b1) ...
Setting up libmpdec2:armhf (2.4.2-2) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-1) ...
Setting up libpython3.7-stdlib:armhf (3.7.6-1) ...
Setting up libtool (2.4.6-11) ...
Setting up libbambamc-dev (0.0.50-3) ...
Setting up m4 (1.4.18-4) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11) ...
Setting up dh-strip-nondeterminism (1.6.3-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up libpython3-stdlib:armhf (3.7.5-3) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up python3.7 (3.7.6-1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libcurl3-gnutls:armhf (7.67.0-2) ...
Setting up python3 (3.7.5-3) ...
Setting up man-db (2.9.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libhts2:armhf (1.9-12) ...
Setting up po-debconf (1.0.21) ...
Setting up samtools (1.9-7) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (12.7.3) ...
Setting up sbuild-build-depends-smalt-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.33.1-5+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-19+rpi1+b1 gcc-9_9.2.1-19+rpi1+b1 libc6-dev_2.29-3+rpi1 libstdc++-9-dev_9.2.1-19+rpi1+b1 libstdc++6_9.2.1-19+rpi1+b1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.46 bash_5.0-5 binutils_2.33.1-5+rpi1 binutils-arm-linux-gnueabihf_2.33.1-5+rpi1 binutils-common_2.33.1-5+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-19+rpi1+b1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.3 debianutils_4.9 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-19+rpi1+b1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-19+rpi1+b1 gcc-9-base_9.2.1-19+rpi1+b1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-4 gzip_1.9-3 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-19+rpi1+b1 libassuan0_2.5.3-7 libatomic1_9.2.1-19+rpi1+b1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbambamc-dev_0.0.50-3 libbambamc0_0.0.50-3 libbinutils_2.33.1-5+rpi1 libblkid1_2.34-0.1 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-3+rpi1 libc-dev-bin_2.29-3+rpi1 libc6_2.29-3+rpi1 libc6-dev_2.29-3+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-19+rpi1+b1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libcurl3-gnutls_7.67.0-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.3 libdeflate0_1.5-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libgcc-9-dev_9.2.1-19+rpi1+b1 libgcc1_1:9.2.1-19+rpi1+b1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.4-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.10-5 libgomp1_9.2.1-19+rpi1+b1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6+b1 libhogweed5_3.5.1+really3.5.1-2 libhts2_1.9-12 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libk5crypto3_1.17-6+b1 libkeyutils1_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-3 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-1 libpsl5_0.20.2-2 libpython3-stdlib_3.7.5-3 libpython3.7-minimal_3.7.6-1 libpython3.7-stdlib_3.7.6-1 libreadline7_7.0-5 libreadline8_8.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 librust-bitflags-dev_1.2.1-1 librust-cloudabi+default-dev_0.0.3-1 librust-cloudabi-dev_0.0.3-1 librust-fuchsia-zircon-dev_0.3.3-2 librust-fuchsia-zircon-sys-dev_0.3.3-2 librust-libc-dev_0.2.62-1 librust-phf-codegen-dev_0.7.23-1 librust-phf-generator-dev_0.7.23-1 librust-phf-shared-dev_0.7.23-2+b1 librust-rand-0.5+alloc-dev_0.5.5-2+rpi1 librust-rand-0.5+std-dev_0.5.5-2+rpi1 librust-rand-0.5-dev_0.5.5-2+rpi1 librust-rand-core-0.2+alloc-dev_0.2.2-1 librust-rand-core-0.2+std-dev_0.2.2-1 librust-rand-core-0.2-dev_0.2.2-1 librust-rand-core-dev_0.3.0-1 librust-siphasher-dev_0.2.3-1 librust-winapi-dev_0.3.6-1 librust-winapi-i686-pc-windows-gnu-dev_0.4.0-1 librust-winapi-x86-64-pc-windows-gnu-dev_0.4.0-1 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.4.2-2+rpi1 libselinux1_2.9-3 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1-1 libss2_1.45.4-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-19+rpi1+b1 libstdc++6_9.2.1-19+rpi1+b1 libsub-override-perl_0.09-2 libsystemd0_243-8+rpi1 libtasn1-6_4.14-3 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-19+rpi1+b1 libuchardet0_0.0.6-3 libudev1_243-8+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_5.7 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkg-config_0.29-6 po-debconf_1.0.21 python3_3.7.5-3 python3-minimal_3.7.5-3 python3.7_3.7.6-1 python3.7-minimal_3.7.6-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 samtools_1.9-7 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-smalt-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 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 Fri Jan 3 19:41:23 2020 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./smalt_0.7.6-9.dsc
dpkg-source: info: extracting smalt in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking smalt_0.7.6.orig.tar.gz
dpkg-source: info: unpacking smalt_0.7.6-9.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 2to3.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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-83bf697a-a40f-4113-83f3-745cc7a93b0a
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package smalt
dpkg-buildpackage: info: source version 0.7.6-9
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
rm -rf test/*.pyc misc/*.pyc test/tmp
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
debian/rules override_dh_autoreconf
make[1]: Entering directory '/<<PKGBUILDDIR>>'
echo "Do nothing - fails because auf broken upstream autoconf stuff"
Do nothing - fails because auf broken upstream autoconf stuff
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# see upstream INSTALL file
CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking for icc... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for ranlib... ranlib
checking for a Python interpreter with version >= 2.6... python3
checking for python3... /usr/bin/python3
checking for python3 version... 3.7
checking for python3 platform... linux
checking for python3 script directory... ${prefix}/lib/python3.7/site-packages
checking for python3 extension module directory... ${exec_prefix}/lib/python3.7/site-packages
checking for samtools... yes
checking for sam_open in -lbam... no
checking for BAMBAMC... yes
checking for gzread in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking semaphore.h usability... yes
checking semaphore.h presence... yes
checking for semaphore.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdint.h... (cached) yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking emmintrin.h usability... no
checking emmintrin.h presence... no
checking for emmintrin.h... no
checking build system type... armv7l-unknown-linux-gnueabihf
checking host system type... armv7l-unknown-linux-gnueabihf
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating test/Makefile
config.status: creating test/data/Makefile
config.status: creating misc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT elib.o -MD -MP -MF .deps/elib.Tpo -c -o elib.o elib.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT filio.o -MD -MP -MF .deps/filio.Tpo -c -o filio.o filio.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT sequence.o -MD -MP -MF .deps/sequence.Tpo -c -o sequence.o sequence.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-score.o -MD -MP -MF .deps/libsgm_a-score.Tpo -c -o libsgm_a-score.o `test -f 'score.c' || echo './'`score.c
score.c:49:21: warning: 'LN0P25' defined but not used [-Wunused-const-variable=]
49 | static const double LN0P25 = -1.386294; /* natural logarithm of 1/4 */
| ^~~~~~
sequence.c: In function 'seqFastqGetConstSequence':
sequence.c:2079:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
2079 | if (length)
| ^~
sequence.c:2081:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
2081 | return NULL;
| ^~~~~~
sequence.c: In function 'seqFastqGetSequence':
sequence.c:2094:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
2094 | if (length)
| ^~
sequence.c:2096:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
2096 | return NULL;
| ^~~~~~
sequence.c: In function 'seqIOopen':
sequence.c:489:5: warning: this statement may fall through [-Wimplicit-fallthrough=]
489 | strcpy(p->fmode, "r");
| ^~~~~~~~~~~~~~~~~~~~~
sequence.c:491:3: note: here
491 | case SEQIO_WRITE_GZIP_FASTA:
| ^~~~
mv -f .deps/filio.Tpo .deps/filio.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-diffstr.o -MD -MP -MF .deps/libsgm_a-diffstr.Tpo -c -o libsgm_a-diffstr.o `test -f 'diffstr.c' || echo './'`diffstr.c
mv -f .deps/libsgm_a-score.Tpo .deps/libsgm_a-score.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-alibuffer.o -MD -MP -MF .deps/libsgm_a-alibuffer.Tpo -c -o libsgm_a-alibuffer.o `test -f 'alibuffer.c' || echo './'`alibuffer.c
mv -f .deps/elib.Tpo .deps/elib.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-alignment.o -MD -MP -MF .deps/libsgm_a-alignment.Tpo -c -o libsgm_a-alignment.o `test -f 'alignment.c' || echo './'`alignment.c
mv -f .deps/libsgm_a-alibuffer.Tpo .deps/libsgm_a-alibuffer.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-sort.o -MD -MP -MF .deps/libsgm_a-sort.Tpo -c -o libsgm_a-sort.o `test -f 'sort.c' || echo './'`sort.c
alignment.c:478:13: warning: 'blankALITRACK' defined but not used [-Wunused-function]
478 | static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp)
| ^~~~~~~~~~~~~
mv -f .deps/libsgm_a-sort.Tpo .deps/libsgm_a-sort.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-array.o -MD -MP -MF .deps/libsgm_a-array.Tpo -c -o libsgm_a-array.o `test -f 'array.c' || echo './'`array.c
mv -f .deps/libsgm_a-array.Tpo .deps/libsgm_a-array.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-interval.o -MD -MP -MF .deps/libsgm_a-interval.Tpo -c -o libsgm_a-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/libsgm_a-alignment.Tpo .deps/libsgm_a-alignment.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-hashidx.o -MD -MP -MF .deps/libsgm_a-hashidx.Tpo -c -o libsgm_a-hashidx.o `test -f 'hashidx.c' || echo './'`hashidx.c
mv -f .deps/libsgm_a-diffstr.Tpo .deps/libsgm_a-diffstr.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-hashhit.o -MD -MP -MF .deps/libsgm_a-hashhit.Tpo -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c
hashidx.c: In function 'countPerfectKey':
hashidx.c:191:77: warning: unused parameter 'tuplectr' [-Wunused-parameter]
191 | static int countPerfectKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
| ~~~~~~~~~~^~~~~~~~
hashidx.c: In function 'countCollisionKey':
hashidx.c:206:79: warning: unused parameter 'tuplectr' [-Wunused-parameter]
206 | static int countCollisionKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
| ~~~~~~~~~~^~~~~~~~
hashidx.c: In function 'collectWords':
hashidx.c:223:74: warning: unused parameter 'tuplectr' [-Wunused-parameter]
223 | static int collectWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
| ~~~~~~~~~~^~~~~~~~
hashidx.c: In function 'countWords':
hashidx.c:265:72: warning: unused parameter 'tuplectr' [-Wunused-parameter]
265 | static int countWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
| ~~~~~~~~~~^~~~~~~~
At top level:
hashidx.c:446:18: warning: 'getWordHisto' defined but not used [-Wunused-function]
446 | static WORDNUM_t getWordHisto(WORDNUM_t *counts, HASHNUM_t n, const HashTable *htp)
| ^~~~~~~~~~~~
hashidx.c:63:19: warning: 'HASHTABFIL_READERRMSG' defined but not used [-Wunused-const-variable=]
63 | static const char HASHTABFIL_READERRMSG[] = "when reading hash table file";
| ^~~~~~~~~~~~~~~~~~~~~
mv -f .deps/libsgm_a-interval.Tpo .deps/libsgm_a-interval.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-segment.o -MD -MP -MF .deps/libsgm_a-segment.Tpo -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.c
segment.c:1375:12: warning: 'checkCANDARRsequential' defined but not used [-Wunused-function]
1375 | static int checkCANDARRsequential(const CANDARR candr, SEGNUM_t *rvc_offs)
| ^~~~~~~~~~~~~~~~~~~~~~
segment.c:1330:13: warning: 'labelSEGCANDWithinInsertRange' defined but not used [-Wunused-function]
1330 | static void labelSEGCANDWithinInsertRange (SEGCAND *candAp, SEGNUM_t nsegA,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mv -f .deps/libsgm_a-hashidx.Tpo .deps/libsgm_a-hashidx.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-smalt.o -MD -MP -MF .deps/smalt-smalt.Tpo -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.c
mv -f .deps/sequence.Tpo .deps/sequence.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-menu.o -MD -MP -MF .deps/smalt-menu.Tpo -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.c
smalt.c: In function 'cleanupSmaltOutput':
smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter]
659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op)
| ~~~~~~~~^~~~~~~
mv -f .deps/libsgm_a-hashhit.Tpo .deps/libsgm_a-hashhit.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-threads.o -MD -MP -MF .deps/smalt-threads.Tpo -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.c
mv -f .deps/libsgm_a-segment.Tpo .deps/libsgm_a-segment.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-infmt.o -MD -MP -MF .deps/smalt-infmt.Tpo -c -o smalt-infmt.o `test -f 'infmt.c' || echo './'`infmt.c
mv -f .deps/smalt-threads.Tpo .deps/smalt-threads.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-results.o -MD -MP -MF .deps/smalt-results.Tpo -c -o smalt-results.o `test -f 'results.c' || echo './'`results.c
results.c: In function 'resultSetInferInsertSize':
results.c:2470:11: warning: self-comparison always evaluates to true [-Wtautological-compare]
2470 | rp->sidx == rp->sidx) {
| ^~
mv -f .deps/smalt-infmt.Tpo .deps/smalt-infmt.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-resultpairs.o -MD -MP -MF .deps/smalt-resultpairs.Tpo -c -o smalt-resultpairs.o `test -f 'resultpairs.c' || echo './'`resultpairs.c
mv -f .deps/smalt-smalt.Tpo .deps/smalt-smalt.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-report.o -MD -MP -MF .deps/smalt-report.Tpo -c -o smalt-report.o `test -f 'report.c' || echo './'`report.c
mv -f .deps/smalt-menu.Tpo .deps/smalt-menu.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-rmap.o -MD -MP -MF .deps/smalt-rmap.Tpo -c -o smalt-rmap.o `test -f 'rmap.c' || echo './'`rmap.c
mv -f .deps/smalt-resultpairs.Tpo .deps/smalt-resultpairs.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-insert.o -MD -MP -MF .deps/smalt-insert.Tpo -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.c
mv -f .deps/smalt-insert.Tpo .deps/smalt-insert.Po
rm -f libseq.a
ar cru libseq.a elib.o filio.o sequence.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libseq.a
rm -f libsgm.a
ar cru libsgm.a libsgm_a-score.o libsgm_a-diffstr.o libsgm_a-alibuffer.o libsgm_a-alignment.o libsgm_a-sort.o libsgm_a-array.o libsgm_a-interval.o libsgm_a-hashidx.o libsgm_a-hashhit.o libsgm_a-segment.o libseq.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libsgm.a
mv -f .deps/smalt-report.Tpo .deps/smalt-report.Po
mv -f .deps/smalt-rmap.Tpo .deps/smalt-rmap.Po
mv -f .deps/smalt-results.Tpo .deps/smalt-results.Po
gcc -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o smalt smalt-smalt.o smalt-menu.o smalt-threads.o smalt-infmt.o smalt-results.o smalt-resultpairs.o smalt-report.o smalt-rmap.o smalt-insert.o libsgm.a libseq.a -lbambamc -lz -lm -lpthread -lz
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making all in test
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
make[4]: Entering directory '/<<PKGBUILDDIR>>/test'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
Making all in misc
make[3]: Entering directory '/<<PKGBUILDDIR>>/misc'
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT simread.o -MD -MP -MF .deps/simread.Tpo -c -o simread.o simread.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT rsample.o -MD -MP -MF .deps/rsample.Tpo -c -o rsample.o rsample.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT fetchseq.o -MD -MP -MF .deps/fetchseq.Tpo -c -o fetchseq.o fetchseq.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT splitreads.o -MD -MP -MF .deps/splitreads.Tpo -c -o splitreads.o splitreads.c
mv -f .deps/rsample.Tpo .deps/rsample.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT mixreads.o -MD -MP -MF .deps/mixreads.Tpo -c -o mixreads.o mixreads.c
mv -f .deps/fetchseq.Tpo .deps/fetchseq.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT splitmates.o -MD -MP -MF .deps/splitmates.Tpo -c -o splitmates.o splitmates.c
mv -f .deps/splitreads.Tpo .deps/splitreads.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT readstats.o -MD -MP -MF .deps/readstats.Tpo -c -o readstats.o readstats.c
simread.c: In function 'simulateSingleRead':
simread.c:534:49: warning: '%s' directive writing up to 4095 bytes into a region of size between 3815 and 4070 [-Wformat-overflow=]
534 | sprintf(read_name, "%s_%9.9i_%s_%9.9u_%lli_%c_%s", readnamprefix, readnum,
| ^~
535 | refnamp, so+1, (long long signed) sidx, (is_reverse)? 'R':'F', alistr);
| ~~~~~~
In file included from /usr/include/stdio.h:867,
from simread.c:29:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 27 or more bytes (assuming 4377) into a destination of size 4096
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
simread.c:534:49: warning: '%s' directive writing up to 4095 bytes into a region of size between 3815 and 4070 [-Wformat-overflow=]
534 | sprintf(read_name, "%s_%9.9i_%s_%9.9u_%lli_%c_%s", readnamprefix, readnum,
| ^~
535 | refnamp, so+1, (long long signed) sidx, (is_reverse)? 'R':'F', alistr);
| ~~~~~~
In file included from /usr/include/stdio.h:867,
from simread.c:29:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 27 or more bytes (assuming 4377) into a destination of size 4096
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mv -f .deps/readstats.Tpo .deps/readstats.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT trunkreads.o -MD -MP -MF .deps/trunkreads.Tpo -c -o trunkreads.o trunkreads.c
mv -f .deps/splitmates.Tpo .deps/splitmates.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT basqcol.o -MD -MP -MF .deps/basqcol.Tpo -c -o basqcol.o basqcol.c
mv -f .deps/trunkreads.Tpo .deps/trunkreads.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT basqual.o -MD -MP -MF .deps/basqual.Tpo -c -o basqual.o basqual.c
mv -f .deps/mixreads.Tpo .deps/mixreads.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT simqual.o -MD -MP -MF .deps/simqual.Tpo -c -o simqual.o simqual.c
mv -f .deps/basqcol.Tpo .deps/basqcol.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT diffstr.o -MD -MP -MF .deps/diffstr.Tpo -c -o diffstr.o `test -f '../src/diffstr.c' || echo './'`../src/diffstr.c
mv -f .deps/simqual.Tpo .deps/simqual.Po
mv -f .deps/basqual.Tpo .deps/basqual.Po
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fetchseq fetchseq.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitreads splitreads.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mixreads mixreads.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitmates splitmates.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o readstats readstats.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o trunkreads trunkreads.o ../src/libseq.a -lz
mv -f .deps/simread.Tpo .deps/simread.Po
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o basqcol basqcol.o basqual.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simread simread.o rsample.o ../src/libsgm.a ../src/libseq.a -lm -lz
mv -f .deps/diffstr.Tpo .deps/diffstr.Po
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simqual simqual.o basqual.o diffstr.o ../src/libseq.a -lm -lz
make[3]: Leaving directory '/<<PKGBUILDDIR>>/misc'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 check VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making check in test
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
make sequenceReverseComplement_test smalt_Xali_test
make[4]: Entering directory '/<<PKGBUILDDIR>>/test'
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT sequenceReverseComplement_test.o -MD -MP -MF .deps/sequenceReverseComplement_test.Tpo -c -o sequenceReverseComplement_test.o sequenceReverseComplement_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-smalt.o -MD -MP -MF .deps/smalt_Xali_test-smalt.Tpo -c -o smalt_Xali_test-smalt.o `test -f '../src/smalt.c' || echo './'`../src/smalt.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-menu.o -MD -MP -MF .deps/smalt_Xali_test-menu.Tpo -c -o smalt_Xali_test-menu.o `test -f '../src/menu.c' || echo './'`../src/menu.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-threads.o -MD -MP -MF .deps/smalt_Xali_test-threads.Tpo -c -o smalt_Xali_test-threads.o `test -f '../src/threads.c' || echo './'`../src/threads.c
../src/smalt.c: In function 'cleanupSmaltOutput':
../src/smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter]
659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op)
| ~~~~~~~~^~~~~~~
mv -f .deps/sequenceReverseComplement_test.Tpo .deps/sequenceReverseComplement_test.Po
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-infmt.o -MD -MP -MF .deps/smalt_Xali_test-infmt.Tpo -c -o smalt_Xali_test-infmt.o `test -f '../src/infmt.c' || echo './'`../src/infmt.c
mv -f .deps/smalt_Xali_test-infmt.Tpo .deps/smalt_Xali_test-infmt.Po
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-results.o -MD -MP -MF .deps/smalt_Xali_test-results.Tpo -c -o smalt_Xali_test-results.o `test -f '../src/results.c' || echo './'`../src/results.c
mv -f .deps/smalt_Xali_test-threads.Tpo .deps/smalt_Xali_test-threads.Po
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-resultpairs.o -MD -MP -MF .deps/smalt_Xali_test-resultpairs.Tpo -c -o smalt_Xali_test-resultpairs.o `test -f '../src/resultpairs.c' || echo './'`../src/resultpairs.c
../src/results.c: In function 'resultSetInferInsertSize':
../src/results.c:2470:11: warning: self-comparison always evaluates to true [-Wtautological-compare]
2470 | rp->sidx == rp->sidx) {
| ^~
mv -f .deps/smalt_Xali_test-smalt.Tpo .deps/smalt_Xali_test-smalt.Po
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-insert.o -MD -MP -MF .deps/smalt_Xali_test-insert.Tpo -c -o smalt_Xali_test-insert.o `test -f '../src/insert.c' || echo './'`../src/insert.c
mv -f .deps/smalt_Xali_test-resultpairs.Tpo .deps/smalt_Xali_test-resultpairs.Po
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-report.o -MD -MP -MF .deps/smalt_Xali_test-report.Tpo -c -o smalt_Xali_test-report.o `test -f '../src/report.c' || echo './'`../src/report.c
mv -f .deps/smalt_Xali_test-menu.Tpo .deps/smalt_Xali_test-menu.Po
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-rmap.o -MD -MP -MF .deps/smalt_Xali_test-rmap.Tpo -c -o smalt_Xali_test-rmap.o `test -f '../src/rmap.c' || echo './'`../src/rmap.c
mv -f .deps/smalt_Xali_test-insert.Tpo .deps/smalt_Xali_test-insert.Po
gcc -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o sequenceReverseComplement_test sequenceReverseComplement_test.o ../src/libseq.a -lz
mv -f .deps/smalt_Xali_test-results.Tpo .deps/smalt_Xali_test-results.Po
mv -f .deps/smalt_Xali_test-report.Tpo .deps/smalt_Xali_test-report.Po
mv -f .deps/smalt_Xali_test-rmap.Tpo .deps/smalt_Xali_test-rmap.Po
gcc -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o smalt_Xali_test smalt_Xali_test-smalt.o smalt_Xali_test-menu.o smalt_Xali_test-threads.o smalt_Xali_test-infmt.o smalt_Xali_test-results.o smalt_Xali_test-resultpairs.o smalt_Xali_test-insert.o smalt_Xali_test-report.o smalt_Xali_test-rmap.o ../src/libsgm.a ../src/libseq.a -lbambamc -lz -lm -lpthread -lz
make[4]: Leaving directory '/<<PKGBUILDDIR>>/test'
make check-TESTS
make[4]: Entering directory '/<<PKGBUILDDIR>>/test'
PASS: splitReads_test.py
PASS: results_split_test.py
PASS: ouform_cigar_test.py
PASS: sample_test.py
PASS: cigar_test.py
PASS: mthread_test.py
PASS: ioform_test.py
PASS: xali_test.py
PASS: bam_cigar_test.py
==================
All 9 tests passed
==================
make[4]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
Making check in misc
make[2]: Entering directory '/<<PKGBUILDDIR>>/misc'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/misc'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# upstream install does install more files than needed
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dwz: debian/smalt/usr/bin/smalt: DWARF compression not beneficial - old size 260362 new size 260532
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/smalt/usr/lib/smalt/test/sequenceReverseComplement_test debian/smalt/usr/bin/smalt were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'smalt' in '../smalt_0.7.6-9_armhf.deb'.
dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-9_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../smalt_0.7.6-9_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-01-06T05:43:36Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
smalt_0.7.6-9_armhf.changes:
----------------------------
Format: 1.8
Date: Fri, 03 Jan 2020 11:44:39 +0100
Source: smalt
Binary: smalt smalt-dbgsym
Architecture: armhf
Version: 0.7.6-9
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Michael R. Crusoe <michael.crusoe@gmail.com>
Description:
smalt - Sequence Mapping and Alignment Tool
Closes: 938501
Changes:
smalt (0.7.6-9) unstable; urgency=medium
.
* Team upload.
.
[ Andreas Tille ]
* Use 2to3 to port to Python3
Closes: #938501
* debhelper-compat 12
* Standards-Version: 4.4.1
* Remove trailing whitespace in debian/changelog
* Use secure URI in debian/watch.
* Use secure URI in Homepage field.
* Set upstream metadata fields: Archive, Bug-Submit.
* autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
.
[ Michael R. Crusoe ]
* Fixed the remaining Python3 issues in test scripts
Checksums-Sha1:
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e754902580ecf370d1602dfd677597e9d0e5b802 93372 smalt_0.7.6-9_armhf.deb
Checksums-Sha256:
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99a1c7868ebf9dbb0eddac9eb3e477edc0d2190b25ff4fb309fa29adc241e24f 93372 smalt_0.7.6-9_armhf.deb
Files:
df79e5635ac38521185f3c380c39aa2e 355308 debug optional smalt-dbgsym_0.7.6-9_armhf.deb
0ef71b51312845fab34c9404d15e2765 5787 science optional smalt_0.7.6-9_armhf.buildinfo
34a6ff48239c23e3dd0882ca26645324 93372 science optional smalt_0.7.6-9_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
smalt-dbgsym_0.7.6-9_armhf.deb
------------------------------
new Debian package, version 2.0.
size 355308 bytes: control archive=640 bytes.
403 bytes, 12 lines control
297 bytes, 3 lines md5sums
Package: smalt-dbgsym
Source: smalt
Version: 0.7.6-9
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 394
Depends: smalt (= 0.7.6-9)
Section: debug
Priority: optional
Description: debug symbols for smalt
Build-Ids: 9c7eaf51a837cb0d260c5389e2b21426aa0787e6 af66c9c897d5ecaf3e9ed086359e2fc7838d8a04
drwxr-xr-x root/root 0 2020-01-03 10:44 ./
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/lib/
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/lib/debug/.build-id/9c/
-rw-r--r-- root/root 323884 2020-01-03 10:44 ./usr/lib/debug/.build-id/9c/7eaf51a837cb0d260c5389e2b21426aa0787e6.debug
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/lib/debug/.build-id/af/
-rw-r--r-- root/root 55340 2020-01-03 10:44 ./usr/lib/debug/.build-id/af/66c9c897d5ecaf3e9ed086359e2fc7838d8a04.debug
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 9056 2020-01-03 10:44 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/smalt.debug
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/share/
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-01-03 10:44 ./usr/share/doc/smalt-dbgsym -> smalt
smalt_0.7.6-9_armhf.deb
-----------------------
new Debian package, version 2.0.
size 93372 bytes: control archive=1224 bytes.
1295 bytes, 30 lines control
334 bytes, 5 lines md5sums
Package: smalt
Version: 0.7.6-9
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 245
Depends: libbambamc0, libc6 (>= 2.29), zlib1g (>= 1:1.2.0.2)
Section: science
Priority: optional
Homepage: https://www.sanger.ac.uk/science/tools/smalt-0
Description: Sequence Mapping and Alignment Tool
SMALT efficiently aligns DNA sequencing reads with a reference genome.
Reads from a wide range of sequencing platforms, for example Illumina,
Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including
paired reads.
.
The software employs a perfect hash index of short words (< 20
nucleotides long), sampled at equidistant steps along the genomic
reference sequences.
.
For each read, potentially matching segments in the reference are
identified from seed matches in the index and subsequently aligned with
the read using a banded Smith-Waterman algorithm.
.
The best gapped alignments of each read is reported including a score
for the reliability of the best mapping. The user can adjust the
trade-off between sensitivity and speed by tuning the length and spacing
of the hashed words.
.
A mode for the detection of split (chimeric) reads is provided.
Multi-threaded program execution is supported.
drwxr-xr-x root/root 0 2020-01-03 10:44 ./
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/bin/
-rwxr-xr-x root/root 189908 2020-01-03 10:44 ./usr/bin/smalt
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/lib/
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/lib/smalt/
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/lib/smalt/test/
-rwxr-xr-x root/root 42584 2020-01-03 10:44 ./usr/lib/smalt/test/sequenceReverseComplement_test
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/share/
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/share/doc/smalt/
-rw-r--r-- root/root 1227 2020-01-03 10:44 ./usr/share/doc/smalt/changelog.Debian.gz
-rw-r--r-- root/root 1182 2020-01-03 08:34 ./usr/share/doc/smalt/copyright
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/share/man/
drwxr-xr-x root/root 0 2020-01-03 10:44 ./usr/share/man/man1/
-rw-r--r-- root/root 884 2020-01-03 10:44 ./usr/share/man/man1/smalt.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 81864
Build-Time: 1893
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 461
Job: smalt_0.7.6-9
Machine Architecture: armhf
Package: smalt
Package-Time: 2419
Source-Version: 0.7.6-9
Space: 81864
Status: successful
Version: 0.7.6-9
--------------------------------------------------------------------------------
Finished at 2020-01-06T05:43:36Z
Build needed 00:40:19, 81864k disc space