I am attempting to install the module Bio::Restriction::Analysis in Strawberry Perl (v5.16.1.1 32 bit) using CPAN. However, it looks like it won't pass a few tests. Portions of CPAN's output are below.
Running Build test
t/Align/AlignStats.t ......................... ok
...
t/Annotation/Annotation.t .................... ok
t/Annotation/AnnotationAdaptor.t ............. ok
t/Assembly/ContigSpectrum.t .................. skipped: The optional module Graph::Undirected (or dependencies thereof)
was not installed
t/Assembly/IO/bowtie.t ....................... skipped: The optional module Bio::Tools::Run::Samtools (or dependencies t
hereof) was not installed
t/Assembly/IO/sam.t .......................... skipped: The optional module Bio::DB::Sam (or dependencies thereof) was n
ot installed
t/Assembly/core.t ............................ 5/890
--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
Can't do inplace edit without backup at Bio/Root/IO.pm line 513.
# Looks like you planned 890 tests but ran 246.
# Looks like your test exited with 25 just after 246.
t/Assembly/core.t ............................ Dubious, test returned 25 (wstat 6400, 0x1900)
Failed 644/890 subtests
...
t/LocalDB/DBFasta.t .......................... 1/17 Can't open sequence index file C:\Users\me\AppData\Local\Temp\2
1EWYU~1\dbfa/directory.index: at Bio/DB/Fasta.pm line 527.
Can't open sequence index file C:\Users\me\AppData\Local\Temp\21EWYU~1\dbfa/directory.index: at Bio/DB/Fasta.pm li
ne 527.
t/LocalDB/DBFasta.t .......................... ok
t/LocalDB/DBQual.t ........................... ok
t/LocalDB/Flat.t ............................. ok
t/LocalDB/Index/Blast.t ...................... ok
t/LocalDB/Index/BlastTable.t ................. ok
t/LocalDB/Index/Index.t ...................... ok
t/LocalDB/Registry.t ......................... ok
t/LocalDB/SeqFeature.t ....................... 2/116 cannot remove directory for C:\Users\me\AppData\Local\Temp\Seq
FeatureLoadHelper_W0QOo5: Directory not empty at Bio/DB/SeqFeature/Store/LoadHelper.pm line 59.
cannot remove directory for C:\Users\me\AppData\Local\Temp\SeqFeatureLoadHelper_P6BE6t: Directory not empty at Bio/
DB/SeqFeature/Store/LoadHelper.pm line 59.
cannot remove directory for C:\Users\me\AppData\Local\Temp\SeqFeatureLoadHelper__f7OZq: Directory not empty at Bio/
DB/SeqFeature/Store/LoadHelper.pm line 59.
cannot unlink file for C:\Users\me\AppData\Local\Temp\edagsNq8fE\sequence.7616.fasta: Permission denied at C:/straw
berry/perl/lib/File/Temp.pm line 902.
cannot remove directory for C:\Users\me\AppData\Local\Temp\edagsNq8fE: Directory not empty at C:/strawberry/perl/li
b/File/Temp.pm line 902.
cannot remove directory for C:\Users\me\AppData\Local\Temp\kiuiljRCJy: Directory not empty at C:/strawberry/perl/li
b/File/Temp.pm line 902.
cannot unlink file for C:\Users\me\AppData\Local\Temp\4gBoAw7k7S\dbfa\7.fa: Permission denied at C:/strawberry/perl
/lib/File/Temp.pm line 902.
cannot remove directory for C:\Users\me\AppData\Local\Temp\4gBoAw7k7S\dbfa: Directory not empty at C:/strawberry/pe
rl/lib/File/Temp.pm line 902.
cannot remove directory for C:\Users\me\AppData\Local\Temp\4gBoAw7k7S: Directory not empty at C:/strawberry/perl/li
b/File/Temp.pm line 902.
cannot remove directory for C:\Users\me\AppData\Local\Temp\xZXsUSasIx: Directory not empty at C:/strawberry/perl/li
b/File/Temp.pm line 902.
t/LocalDB/SeqFeature.t ....................... ok
t/LocalDB/transfac_pro.t ..................... 4/115 cannot unlink file for C:\Users\me\AppData\Local\Temp\fdtykE6R
Qb\id2names: Permission denied at C:/strawberry/perl/lib/File/Temp.pm line 902.
cannot unlink file for C:\Users\me\AppData\Local\Temp\fdtykE6RQb\nodes: Permission denied at C:/strawberry/perl/lib
/File/Temp.pm line 902.
cannot remove directory for C:\Users\me\AppData\Local\Temp\fdtykE6RQb: Directory not empty at C:/strawberry/perl/li
b/File/Temp.pm line 902.
t/LocalDB/transfac_pro.t ..................... ok
t/Map/Cyto.t ................................. ok
t/Map/Linkage.t .............................. ok
t/Map/Map.t .................................. ok
t/Map/MapIO.t ................................ ok
t/Map/MicrosatelliteMarker.t ................. ok
t/Map/Physical.t ............................. ok
t/Matrix/IO/masta.t .......................... ok
t/Matrix/IO/psm.t ............................ ok
t/Matrix/InstanceSite.t ...................... ok
t/Matrix/Matrix.t ............................ ok
t/Matrix/ProtMatrix.t ........................ ok
t/Matrix/ProtPsm.t ........................... ok
t/Matrix/SiteMatrix.t ........................ ok
t/Ontology/GOterm.t .......................... skipped: The optional module Graph::Directed (or dependencies thereof) wa
s not installed
t/Ontology/GraphAdaptor.t .................... skipped: The optional module Graph (or dependencies thereof) was not inst
alled
t/Ontology/IO/go.t ........................... skipped: The optional module Graph (or dependencies thereof) was not inst
alled
t/Ontology/IO/interpro.t ..................... skipped: The optional module XML::Parser::PerlSAX (or dependencies thereo
f) was not installed
t/Ontology/IO/obo.t .......................... skipped: The optional module Graph (or dependencies thereof) was not inst
alled
t/Ontology/Ontology.t ........................ skipped: The optional module Graph (or dependencies thereof) was not inst
alled
t/Ontology/OntologyEngine.t .................. skipped: The optional module Graph::Directed (or dependencies thereof) wa
s not installed
t/Ontology/OntologyStore.t ................... skipped: The optional module Graph (or dependencies thereof) was not inst
alled
t/Ontology/Relationship.t .................... skipped: The optional module Graph::Directed (or dependencies thereof) wa
s not installed
t/Ontology/RelationshipType.t ................ skipped: The optional module Graph::Directed (or dependencies thereof) wa
s not installed
t/Ontology/Term.t ............................ skipped: The optional module Graph::Directed (or dependencies thereof) wa
s not installed
...
t/Root/RootI.t ............................... ok
t/Root/RootIO.t .............................. 1/67
# Failed test 'executable file'
# at t/Root/RootIO.t line 55.
Can't do inplace edit without backup at Bio/Root/IO.pm line 513.
# Looks like you planned 67 tests but ran 43.
# Looks like you failed 1 test of 43 run.
# Looks like your test exited with 25 just after 43.
Error removing C:\Users\me\AppData\Local\Temp\9eXZD151tL at C:/strawberry/perl/lib/File/Temp.pm line 890.
t/Root/RootIO.t .............................. Dubious, test returned 25 (wstat 6400, 0x1900)
Failed 25/67 subtests
...
t/SearchIO/erpin.t ........................... 1/91 defined(@array) is deprecated at Bio\Search\Hit\ModelHit.pm line 355
.
(Maybe you should just omit the defined()?)
t/SearchIO/erpin.t ........................... ok
t/SearchIO/exonerate.t ....................... ok
t/SearchIO/fasta.t ........................... ok
t/SearchIO/gmap_f9.t ......................... ok
t/SearchIO/hmmer.t ........................... ok
t/SearchIO/hmmer_pull.t ...................... ok
t/SearchIO/infernal.t ........................ 1/412 defined(@array) is deprecated at Bio\Search\Hit\ModelHit.pm line 35
5.
(Maybe you should just omit the defined()?)
t/SearchIO/infernal.t ........................ ok
t/SearchIO/megablast.t ....................... ok
t/SearchIO/psl.t ............................. ok
t/SearchIO/rnamotif.t ........................ 1/60 defined(@array) is deprecated at Bio\Search\Hit\ModelHit.pm line 355
.
(Maybe you should just omit the defined()?)
t/SearchIO/rnamotif.t ........................ ok
t/SearchIO/sim4.t ............................ ok
t/SearchIO/waba.t ............................ ok
t/SearchIO/wise.t ............................ ok
...
Test Summary Report
-------------------
t/Assembly/core.t (Wstat: 6400 Tests: 246 Failed: 0)
Non-zero exit status: 25
Parse errors: Bad plan. You planned 890 tests but ran 246.
t/Root/RootIO.t (Wstat: 6400 Tests: 43 Failed: 1)
Failed test: 11
Non-zero exit status: 25
Parse errors: Bad plan. You planned 67 tests but ran 43.
Files=349, Tests=17876, 330 wallclock secs ( 3.99 usr + 1.55 sys = 5.54 CPU)
Result: FAIL
Failed 2/349 test programs. 1/17876 subtests failed.
CJFIELDS/BioPerl-1.6.901.tar.gz
C:\strawberry\perl\bin\perl.exe ./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports CJFIELDS/BioPerl-1.6.901.tar.gz
Running Build install
make test had returned bad status, won't install without force
Stopping: 'install' failed for 'Bio::Restriction::Analysis'.
Failed during this command:
CJFIELDS/BioPerl-1.6.901.tar.gz : make_test NO
I am doing a simple "install Bio::Restriction::Analysis" in CPAN, and accepting all of the default installation options. I had thought BioPerl was bundled with Strawberry Perl, so that may be one of the problems.
