[Bioperl-guts-l] [Bug 2313] New: './Build test' stalls from current cvs bioperl-run

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Jun 7 10:14:31 EDT 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2313

           Summary: './Build test' stalls  from current cvs bioperl-run
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bioperl-run
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: mmokrejs at ribosome.natur.cuni.cz


t/Amap........................ok                                             
        8/18 skipped: various reasons
t/AnalysisFactory_soap........ok                                             
t/Analysis_soap...............ok                                             
t/Blat........................ok 1/11blat  program not found. Skipping tests 2
to 11.
t/Blat........................ok                                             
        10/11 skipped: various reasons
t/Clustalw....................ok                                             
t/Coil........................Need to define env variable COILSDIR to run test
at t/Coil.t line 27.
t/Coil........................ok                                             
        4/4 skipped: various reasons
t/Consense....................ok                                             
t/DBA.........................ok 1/15Find start end points: [0,17][209,222]
Score 109962
Recovering alignment: Alignment recoveredit read offffls done 78%
Find start end points: [0,0][209,195] Score 99400
Recovering alignment: Alignment recovered read offffffls done 86%
t/DBA.........................ok 7/15[0,17][209,222] Score 109962            
Recovering alignment: Alignment recoveredit read offffls done 78%
t/DBA.........................ok                                             
t/DrawGram....................ok                                             
t/DrawTree....................ok                                             
t/EMBOSS......................ok                                             
t/Eponine.....................ok                                             
        5/5 skipped: various reasons
t/Exonerate...................ok                                             
        87/88 skipped: various reasons
t/FootPrinter.................FootPrinter program not found. Skipping tests 1
to 22.
t/FootPrinter.................ok                                             
        22/22 skipped: various reasons
t/Genemark.hmm.prokaryotic....ok 1/99# Looks like you planned 99 tests but only
ran 98.
t/Genemark.hmm.prokaryotic....dubious                                        
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED test 99
        Failed 1/99 tests, 98.99% okay (less 95 skipped tests: 3 okay, 3.03%)
t/Genewise....................ok                                             
t/Genscan.....................Need to define env variable GENSCANDIR to run
test at t/Genscan.t line 28.
t/Genscan.....................ok                                             
        4/4 skipped: various reasons
t/Glimmer2....................ok 1/217# Looks like you planned 217 tests but
only ran 203.
t/Glimmer2....................dubious                                        
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 204-217
        Failed 14/217 tests, 93.55% okay (less 199 skipped tests: 4 okay,
1.84%)
t/Glimmer3....................ok 1/111# Looks like you planned 111 tests but
only ran 110.
t/Glimmer3....................dubious                                        
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED test 111
        Failed 1/111 tests, 99.10% okay (less 106 skipped tests: 4 okay, 3.60%)
t/Gumby.......................ok                                             
        111/124 skipped: various reasons
t/Hmmer.......................ok                                             
t/Hyphy.......................Subroutine no_param_checks redefined at
/home/mmokrejs/proj/bioperl/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Hyphy/Base.pm
line 474.
"my" variable $rc masks earlier declaration in same scope at t/Hyphy.t line 80.
"my" variable $results masks earlier declaration in same scope at t/Hyphy.t
line 80.
"my" variable $rc masks earlier declaration in same scope at t/Hyphy.t line 86.
"my" variable $results masks earlier declaration in same scope at t/Hyphy.t
line 86.
"my" variable $rc masks earlier declaration in same scope at t/Hyphy.t line 92.
"my" variable $results masks earlier declaration in same scope at t/Hyphy.t
line 92.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: unable to find or run executable for 'HYPHY'
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::Tools::Run::Phylo::Hyphy::SLAC::run
/home/mmokrejs/proj/bioperl/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm:199
STACK: t/Hyphy.t:74
-----------------------------------------------------------
t/Hyphy.......................dubious                                        
        Test returned status 2 (wstat 512, 0x200)
        after all the subtests completed successfully
t/Kalign......................ok 1/6amap program not found. Skipping tests 2 to
6.
t/Kalign......................ok                                             
        5/6 skipped: various reasons
t/LVB.........................ok 1/20LVB program not found. Skipping tests 3 to
20.
t/LVB.........................ok                                             
        18/20 skipped: various reasons
t/Lagan.......................ok 1/7                                         
-------------------- WARNING ---------------------
MSG: Environment variable LAGAN_DIR must be set, even if the lagan executables
are in your path
---------------------------------------------------
lagan program not found. Skipping tests 3 to 7.
t/Lagan.......................ok                                             
        5/7 skipped: various reasons
t/MAFFT.......................ok 1/15mafft program not found. Skipping tests 3
to 15.
t/MAFFT.......................ok                                             
        13/15 skipped: various reasons
t/Mdust.......................ok 1/2Mdust not installed Skipping tests 2 to 2.
t/Mdust.......................ok                                             
        1/2 skipped: various reasons
t/Molphy......................Molphy package not installed. Skipping tests 1 to
7.
t/Molphy......................ok                                             
        7/7 skipped: various reasons
t/Muscle......................ok 1/12muscle program not found. Skipping tests 3
to 12.
t/Muscle......................ok                                             
        10/12 skipped: various reasons
t/Neighbor....................FAILED tests 16-17                             
        Failed 2/15 tests, 86.67% okay
t/Njtree......................
-------------------- WARNING ---------------------
MSG: 11 unmapped ids between the aln and the tree
CAEELXX,DROME,CAEBR,HUMAN,CANFA,MOUSE,ANOGA,CAEREXX,BRARE,SCHMAXX,DROPS
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/home/mmokrejs/proj/bioperl/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Njtree/Best.pm
line 272, <GEN1> line 1.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: unable to find or run executable for 'njtree'
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::Tools::Run::Phylo::Njtree::Best::run
/home/mmokrejs/proj/bioperl/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Njtree/Best.pm:284
STACK: t/Njtree.t:76
-----------------------------------------------------------
t/Njtree......................dubious                                        
        Test returned status 2 (wstat 512, 0x200)
        after all the subtests completed successfully
t/PAML........................ok 1/18PAML not is installed. skipping tests 2 to
18
t/PAML........................ok                                             
        17/18 skipped: various reasons
t/PhastCons...................ok                                             
        166/181 skipped: various reasons
t/Phrap.......................ok 1/5Phrap program not found. Skipping tests 4
to 5.
t/Phrap.......................ok                                             
        2/5 skipped: various reasons
t/Pise........................Subroutine stdout redefined at
/home/mmokrejs/proj/bioperl/bioperl-run/blib/lib/Bio/Tools/Run/PiseJob.pm line
609.
Subroutine stderr redefined at
/home/mmokrejs/proj/bioperl/bioperl-run/blib/lib/Bio/Tools/Run/PiseJob.pm line
644.
t/Pise........................ok 1/11Use of uninitialized value in hash element
at
/home/mmokrejs/proj/bioperl/bioperl-run/blib/lib/Bio/Tools/Run/PiseJobParser.pm
line 181.
Use of uninitialized value in hash element at
/home/mmokrejs/proj/bioperl/bioperl-run/blib/lib/Bio/Tools/Run/PiseJobParser.pm
line 181.
Use of uninitialized value in hash element at
/home/mmokrejs/proj/bioperl/bioperl-run/blib/lib/Bio/Tools/Run/PiseJobParser.pm
line 181.
Use of uninitialized value in hash element at
/home/mmokrejs/proj/bioperl/bioperl-run/blib/lib/Bio/Tools/Run/PiseJobParser.pm
line 181.
Use of uninitialized value in hash element at
/home/mmokrejs/proj/bioperl/bioperl-run/blib/lib/Bio/Tools/Run/PiseJobParser.pm
line 181.
Use of uninitialized value in hash element at
/home/mmokrejs/proj/bioperl/bioperl-run/blib/lib/Bio/Tools/Run/PiseJobParser.pm
line 197.
Use of uninitialized value in hash element at
/home/mmokrejs/proj/bioperl/bioperl-run/blib/lib/Bio/Tools/Run/PiseJobParser.pm
line 197.
Use of uninitialized value in hash element at
/home/mmokrejs/proj/bioperl/bioperl-run/blib/lib/Bio/Tools/Run/PiseJobParser.pm
line 197.


and now the testing does not continue, system is idle and the application is
maybe waiting for some input.

root     10680  5769  0 16:07 pts/1    00:00:01 /usr/bin/perl5.8.8 ./Build test
root     10857 10680  0 16:08 pts/1    00:00:00 /usr/bin/perl5.8.8 -w t/Pise.t


I would also suggest to cleanup a bit the output of the testsuite, and fix
the programming errors. ;)


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