[Debian-med-packaging] Bug#484201: libgo-perl: FTBFS: t/t270oborel_in_owl......sh: xsltproc: command not found

Tue Jun 3 00:20:22 UTC 2008

Package: libgo-perl
Version: 0.08-1
Severity: serious
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20080602 qa-ftbfs
Justification: FTBFS on i386

Hi,

During a rebuild of all packages in sid, your package failed to build on
i386.

Relevant part:
> make[1]: Entering directory `/build/user-libgo-perl_0.08-1-amd64-N1Ov_G/libgo-perl-0.08-1'
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/t010build..............ok
> t/t020paths..............ok
> t/t030detecterror........ok
> t/t050oboformat..........ok
> t/t060oboformat2.........ok
> t/t070parseannot2obj.....ok
> t/t080gofmt2.............ok
> t/t100roundtrip..........ok
> t/t110basic..............Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 484, <GEN0> line 81.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 485, <GEN0> line 81.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 516, <GEN0> line 81.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 484, <GEN0> line 82.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 485, <GEN0> line 82.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 516, <GEN0> line 82.
> ok
> t/t130relations..........Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 484, <GEN0> line 19.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 485, <GEN0> line 19.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 516, <GEN0> line 19.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 484, <GEN1> line 81.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 485, <GEN1> line 81.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 516, <GEN1> line 81.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 484, <GEN1> line 82.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 485, <GEN1> line 82.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 516, <GEN1> line 82.
> ok
> t/t140subgraph...........ok
> t/t150xref...............ok
> t/t160logicaldef.........ok
> t/t170chadoxml...........sh: xsltproc: command not found
> problem running: xsltproc GO/xsl/oboxml_to_chadoxml.xsl TMP.20625.llm.obo-1.xml > TMP.20625.llm.obo-2.xml at GO/Parsers/base_parser.pm line 419
> 	GO::Parsers::base_parser::xsltproc('GO/xsl/oboxml_to_chadoxml.xsl', 'TMP.20625.llm.obo-1.xml', 'TMP.20625.llm.obo-2.xml') called at GO/Parsers/base_parser.pm line 385
> 	GO::Parsers::base_parser::parse('GO::Parsers::obo_parser=HASH(0x840f018)', './t/data/llm.obo') called at t/t170chadoxml.t line 44
> dubious
> 	Test returned status 127 (wstat 32512, 0x7f00)
> DIED. FAILED tests 1-9
> 	Failed 9/9 tests, 0.00% okay
> t/t180ncbi_taxonomy......ok
> t/t200impliedlinks.......ok
> t/t210cache..............Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 484, <GEN0> line 81.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 485, <GEN0> line 81.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 516, <GEN0> line 81.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 484, <GEN0> line 82.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 485, <GEN0> line 82.
> Use of uninitialized value $txt in substitution (s///) at GO/Parsers/obo_text_parser.pm line 516, <GEN0> line 82.
> ok
> t/t220xref_esc...........ok
> t/t230term_expression....ok
> t/t240ga2obj.............ok
> t/t260oborel_in_chado....sh: xsltproc: command not found
> problem running: xsltproc GO/xsl/oboxml_to_chadoxml.xsl TMP.20634.go-with-local-id-mapping.obo-1.xml > TMP.20634.go-with-local-id-mapping.obo-2.xml at GO/Parsers/base_parser.pm line 419
> 	GO::Parsers::base_parser::xsltproc('GO/xsl/oboxml_to_chadoxml.xsl', 'TMP.20634.go-with-local-id-mapping.obo-1.xml', 'TMP.20634.go-with-local-id-mapping.obo-2.xml') called at GO/Parsers/base_parser.pm line 385
> 	GO::Parsers::base_parser::parse('GO::Parsers::obo_parser=HASH(0x840e670)', './t/data/go-with-local-id-mapping.obo') called at t/t260oborel_in_chado.t line 44
> dubious
> 	Test returned status 127 (wstat 32512, 0x7f00)
> DIED. FAILED tests 1-6
> 	Failed 6/6 tests, 0.00% okay
> t/t270oborel_in_owl......sh: xsltproc: command not found
> problem running: xsltproc GO/xsl/oboxml_to_owl.xsl TMP.20637.go-with-local-id-mapping.obo-1.xml > TMP.20637.go-with-local-id-mapping.obo-2.xml at GO/Parsers/base_parser.pm line 419
> 	GO::Parsers::base_parser::xsltproc('GO/xsl/oboxml_to_owl.xsl', 'TMP.20637.go-with-local-id-mapping.obo-1.xml', 'TMP.20637.go-with-local-id-mapping.obo-2.xml') called at GO/Parsers/base_parser.pm line 385
> 	GO::Parsers::base_parser::parse('GO::Parsers::obo_parser=HASH(0x840e090)', './t/data/go-with-local-id-mapping.obo') called at t/t270oborel_in_owl.t line 44
> dubious
> 	Test returned status 127 (wstat 32512, 0x7f00)
> DIED. FAILED tests 1-4
> 	Failed 4/4 tests, 0.00% okay
> Failed Test             Stat Wstat Total Fail  List of Failed
> -------------------------------------------------------------------------------
> t/t170chadoxml.t         127 32512     9   18  1-9
> t/t260oborel_in_chado.t  127 32512     6   12  1-6
> t/t270oborel_in_owl.t    127 32512     4    8  1-4
> Failed 3/22 test scripts. 19/129 subtests failed.
> Files=22, Tests=129,  6 wallclock secs ( 6.23 cusr +  0.29 csys =  6.52 CPU)
> Failed 3/22 test programs. 19/129 subtests failed.
> make[1]: *** [test_dynamic] Error 127

The full build log is available from:
   http://people.debian.org/~lucas/logs/2008/06/02

This rebuild was done with gcc 4.3 instead of gcc 4.2, because gcc 4.3
is now the default on most architectures (even if it's not the case on
i386 yet).  Consequently, many failures are caused by the switch to gcc
4.3.
If you determine that this failure is caused by gcc 4.3, feel free to
downgrade this bug to 'important' if your package is only built on i386,
and this bug is specific to gcc 4.3 (i.e the package builds fine with
gcc 4.2).

A list of current common problems and possible solutions is available at 
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on about 50 AMD64 nodes
of the Grid'5000 platform, using a clean chroot containing a sid i386
environment.  Internet was not accessible from the build systems.

-- 
| Lucas Nussbaum
| lucas at lucas-nussbaum.net   http://www.lucas-nussbaum.net/ |
| jabber: lucas at nussbaum.fr             GPG: 1024D/023B3F4F |