[Debian-med-packaging] Bug#809120: ncbi-blast+: FTBFS when built with dpkg-buildpackage -A (cp: target is not a directory)

[Santiago Vila]

Package: src:ncbi-blast+
Version: 2.2.31-2
User: sanvila at debian.org
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.