ncbi-blast+ version 2.2.25-3 failed to build on i386

Bug #803185 reported by Stefano Rivera on 2011-06-28
10
This bug affects 1 person
Affects Status Importance Assigned to Milestone
ncbi-blast+ (Debian)
Fix Released
Unknown
ncbi-blast+ (Ubuntu)
Medium
Unassigned

Bug Description

ncbi-blast+ version 2.2.25-3 failed to build on i386
Link to failed build: https://launchpad.net/ubuntu/+source/ncbi-blast+/2.2.25-3/+build/2562052

Direct link to the build log: https://launchpad.net/ubuntu/+source/ncbi-blast+/2.2.25-3/+build/2562052/+files/buildlog_ubuntu-oneiric-i386.ncbi-blast%2B_2.2.25-3_FAILEDTOBUILD.txt.gz

This log snippet might be of interest, since it triggered the matcher 'Purging chroot-autobuild'.
Excerpt 58224 lines into the build log:

rm -f bdbloader_unit_test .bdbloader_unit_test.stamp
make[6]: Leaving directory `/build/buildd/ncbi-blast+-2.2.25/c++/BUILD/build/algo/blast/unit_tests/blastdb'
FAILED: src/algo/blast/unit_tests/blastdb/Makefile.bdbloader_unit_test.app
make[5]: *** [all.nonusr] Error 3
make[5]: Leaving directory `/build/buildd/ncbi-blast+-2.2.25/c++/BUILD/build/algo/blast/unit_tests/blastdb'
make[4]: *** [all.needs-reqs] Error 2
make[4]: Leaving directory `/build/buildd/ncbi-blast+-2.2.25/c++/BUILD/build/algo/blast/unit_tests/blastdb'
make[3]: *** [bdbloader_unit_test.exe.real] Error 2
make[3]: Leaving directory `/build/buildd/ncbi-blast+-2.2.25/c++/BUILD/build'
make[2]: *** [ptb_all] Error 2
make[2]: Leaving directory `/build/buildd/ncbi-blast+-2.2.25/c++/BUILD/build'
make[1]: *** [override_dh_auto_build] Error 2
make[1]: Leaving directory `/build/buildd/ncbi-blast+-2.2.25'
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
******************************************************************************
Build finished at 20110611-1058
FAILED [dpkg-buildpackage died]
Purging chroot-autobuild/build/buildd/ncbi-blast+-2.2.25

Related branches

Changed in ncbi-blast+ (Ubuntu):
importance: Undecided → Medium
Julian Taylor (jtaylor) wrote :

most of the private libs of this package are underlinked:
$ ldd -r /usr/lib/ncbi-blast+/*so 2>&1 | grep -c undefined
8291

fixing this package seems like a lot of work and looking at the dependencies it does not seem like one gains much.
I recommend building this one without --as-needed

Launchpad Janitor (janitor) wrote :

This bug was fixed in the package ncbi-blast+ - 2.2.25-3ubuntu1

---------------
ncbi-blast+ (2.2.25-3ubuntu1) oneiric; urgency=low

  * debian/rules: disable --as-needed build (LP: #803185)
    almost all private libs are underlinked, fixing them is not worth the
    effort
 -- Julian Taylor <email address hidden> Mon, 18 Jul 2011 16:02:34 +0200

Changed in ncbi-blast+ (Ubuntu):
status: New → Fix Released
Changed in ncbi-blast+ (Debian):
status: Unknown → New
Changed in ncbi-blast+ (Debian):
status: New → Fix Released
Heidi Pagan (heidijtp) wrote :

I am having this error while trying to install the rmblast package 2.2.23 in ubuntu (modified version of NCBI Blast to use with RepeatMasker: http://www.repeatmasker.org/RMBlast.html).

Is there a fix for this? Here is the error I get after executing 'make':

make[8]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi/driver'
make[7]: *** [all.nonusr] Error 2
make[7]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi/driver'
make[6]: *** [all.real] Error 2
make[6]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi/driver'
make[5]: *** [all_r.needs-reqs] Error 2
make[5]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi/driver'
make[4]: *** [all_r.real] Error 5
make[4]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi'
make[3]: *** [all_r.needs-reqs] Error 2
make[3]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build/dbapi'
make[2]: *** [all_r.real] Error 5
make[2]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build'
make[1]: *** [all_r.needs-reqs] Error 2
make[1]: Leaving directory `/usr/local/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC461-ReleaseMT/build'
make: *** [all] Error 2

Thanks for any suggestions!

Julian Taylor (jtaylor) wrote :

have you tried applying a similar patch to the one used to fix this bug? (=setting LDFLAGS=-Wl,--no-as-needed)

Heidi Pagan (heidijtp) wrote :

Julian - thanks for the info, and sorry for the delayed response.
I barely know enough to get around linux, and know nothing about using a patch. Is this part of the 'make' file command? Or do I add it into the Makefile somewhere?

Julian Taylor (jtaylor) wrote :

this might work:
make LDFLAGS="-Wl,--no-as-needed"

Heidi Pagan (heidijtp) wrote :

Thanks so much for the fast response, but unfortunately I am still getting the same error message. Combing back through the output, I noticed another error further up:

In file included from /home/hjtp/Downloads/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/include/dbapi/driver/impl/dbapi_impl_result.hpp:35:0,
                 from /home/hjtp/Downloads/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/src/dbapi/driver/public.cpp:34:
/home/hjtp/Downloads/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp:234:32: error: reference ‘m_Conn’ cannot be declared ‘mutable’ [-fpermissive]
make[8]: *** [public.o] Error 1

Heidi Pagan (heidijtp) wrote :

Helpful suggestions from another forum led me to this solution:
Add -fpermissive to your CXXFLAGS

Seth Munholland (munholl) wrote :

I'm having the same issue and trying to do the same, but I'm inexperienced with linux. How do you add -fpermissive to CXXFLAGS?

Heidi Pagan (heidijtp) wrote :

Seth,

You can add it right into the 'make' command after configuration:

make CXXFLAGS="-fpermissive"

Seth Munholland (munholl) wrote :

That did it, thank you very much Heidi!

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