Your message dated Mon, 28 Dec 2015 16:23:57 +0000
with message-id <[email protected]>
and subject line Bug#809120: fixed in ncbi-blast+ 2.2.31-3
has caused the Debian Bug report #809120,
regarding ncbi-blast+: FTBFS when built with dpkg-buildpackage -A (cp: target
is not a directory)
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
809120: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=809120
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:ncbi-blast+
Version: 2.2.31-2
User: [email protected]
Usertags: binary-indep
Severity: important
Dear maintainer:
I tried to build this package with "dpkg-buildpackage -A"
(i.e. only architecture-independent packages), and it failed:
--------------------------------------------------------------------------------
[...]
debian/rules build-indep
dh build-indep -Dc++ --with autotools_dev --with quilt
dh_testdir -i -O-Dc\+\+
dh_autotools-dev_updateconfig -i -O-Dc\+\+
dh_quilt_patch -i -O-Dc\+\+
Applying patch enable_clean_after_failed_compile
patching file c++/src/build-system/new_module.sh.in
Applying patch legacy_rename_rpsblast
patching file c++/src/app/blast/legacy_blast.pl
Applying patch fix_lib_deps
[... snipped ...]
Done.
/build/ncbi-blast+-jlDlzM/ncbi-blast+-2.2.31/c++/BUILD/build/check.sh: 1:
/build/ncbi-blast+-jlDlzM/ncbi-blast+-2.2.31/c++/BUILD/build/check.sh: uptime:
not found
OK -- [serial/datatool] datatool.sh (real 0.38, user 0.20, sys 0.01)
/build/ncbi-blast+-jlDlzM/ncbi-blast+-2.2.31/c++/BUILD/build/check.sh: 1:
/build/ncbi-blast+-jlDlzM/ncbi-blast+-2.2.31/c++/BUILD/build/check.sh: uptime:
not found
SKP -- [serial/datatool] datatool_xml.sh
/build/ncbi-blast+-jlDlzM/ncbi-blast+-2.2.31/c++/BUILD/build/check.sh: 1:
/build/ncbi-blast+-jlDlzM/ncbi-blast+-2.2.31/c++/BUILD/build/check.sh: uptime:
not found
OK -- [objtools/blast/gene_info_reader/unit_test] gene_info_unit_test
(real 0.02, user 0.00, sys 0.00)
/build/ncbi-blast+-jlDlzM/ncbi-blast+-2.2.31/c++/BUILD/build/check.sh: 1:
/build/ncbi-blast+-jlDlzM/ncbi-blast+-2.2.31/c++/BUILD/build/check.sh: uptime:
not found
OK -- [algo/blast/unit_tests/api] blastdiag_unit_test (real 0.02, user
0.00, sys 0.00)
/build/ncbi-blast+-jlDlzM/ncbi-blast+-2.2.31/c++/BUILD/build/check.sh: 1:
/build/ncbi-blast+-jlDlzM/ncbi-blast+-2.2.31/c++/BUILD/build/check.sh: uptime:
not found
OK -- [algo/blast/unit_tests/api] aascan_unit_test (real 1.92, user 0.52,
sys 0.03)
Succeeded : 4
Timeout : 0
Failed : 0
Absent : 1
******** ALL TESTS COMPLETED SUCCESSFULLY ********
make[3]: Leaving directory
'/build/ncbi-blast+-jlDlzM/ncbi-blast+-2.2.31/c++/BUILD/build'
make[2]: Leaving directory '/build/ncbi-blast+-jlDlzM/ncbi-blast+-2.2.31/c++'
c++/BUILD/build/check.sh concat_err
cat c++/BUILD/build/check.sh.out_err
make[1]: Leaving directory '/build/ncbi-blast+-jlDlzM/ncbi-blast+-2.2.31'
fakeroot debian/rules binary-indep
dh binary-indep -Dc++ --with autotools_dev --with quilt
dh_testroot -i -O-Dc\+\+
dh_prep -i -O-Dc\+\+
dh_installdirs -i -O-Dc\+\+
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/ncbi-blast+-jlDlzM/ncbi-blast+-2.2.31'
cp c++/BUILD/lib/*.so debian/ncbi-blast+/usr/lib/ncbi-blast+/
cp: target 'debian/ncbi-blast+/usr/lib/ncbi-blast+/' is not a directory
debian/rules:63: recipe for target 'override_dh_auto_install' failed
make[1]: *** [override_dh_auto_install] Error 1
make[1]: Leaving directory '/build/ncbi-blast+-jlDlzM/ncbi-blast+-2.2.31'
debian/rules:104: recipe for target 'binary-indep' failed
make: *** [binary-indep] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-indep gave error exit
status 2
--------------------------------------------------------------------------------
Sorry not to have a fix, as I am reporting many bugs similar to
this one. The common hints are:
* If the only architecture-independent packages are dummy transitional
ones and they were released with jessie, the easy fix is to drop them
now.
* When using "dh", it is allowed to use (independently)
optional targets override_dh_foo-arch and override_dh_foo-indep
(for several values of "foo").
Once that both "dpkg-buildpackage -A" and "dpkg-buildpackage -B" work
properly, the package would be suitable to be uploaded in source-only
form if you wish.
Thanks.
--- End Message ---
--- Begin Message ---
Source: ncbi-blast+
Source-Version: 2.2.31-3
We believe that the bug you reported is fixed in the latest version of
ncbi-blast+, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated ncbi-blast+ package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Mon, 28 Dec 2015 12:32:23 +0100
Source: ncbi-blast+
Binary: ncbi-blast+ ncbi-blast+-legacy
Architecture: source
Version: 2.2.31-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
ncbi-blast+ - next generation suite of BLAST sequence search tools
ncbi-blast+-legacy - NCBI Blast legacy call script
Closes: 809120
Changes:
ncbi-blast+ (2.2.31-3) unstable; urgency=medium
.
* Drop explicite mentioning of quilt
* Enable building architecture independent package separately
Closes: #809120
* Override false lintian error
* DEP5 fixes
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