[Bioperl-l] BioPerl Installation on Suse 11.0 Failed ?
Imtiaz M.
biobrain at gmail.com
Wed Nov 26 13:52:39 UTC 2008
I am trying to install bioperl 1.4 both from CPAN and from local
directory after downloading but i am unable to get it running.
here is some log of installation work. Please give me some suggestions
how to proceed
perl Makefile.PL
Generated sub tests. go make show_tests to see available subtests
*** Script Install Section ****
Bioperl comes with a number of useful scripts which you may wish to install.
Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a]
cannot unlink file for scripts_temp/bp_pg_bulk_load_gff.pl: Permission denied at
Makefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_pg_bulk_load_gff.pl: P
ermission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_process_gadfly.pl: Permission denied at M
akefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_process_gadfly.pl: Per
mission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_composite_LD.pl: Permission denied at Mak
efile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_composite_LD.pl: Permi
ssion denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_index.pl: Permission denied at Makefile.P
L line 118
cannot restore permissions to 0100555 for scripts_temp/bp_index.pl: Permission d
enied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_dbsplit.pl: Permission denied at Makefile
.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_dbsplit.pl: Permission
denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_filter_search.pl: Permission denied at Ma
kefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_filter_search.pl: Perm
ission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_bioflat_index.pl: Permission denied at Ma
kefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_bioflat_index.pl: Perm
ission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_pairwise_kaks.pl: Permission denied at Ma
kefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_pairwise_kaks.pl: Perm
ission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_mutate.pl: Permission denied at Makefile.
PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_mutate.pl: Permission
denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_taxid4species.pl: Permission denied at Ma
kefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_taxid4species.pl: Perm
ission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_nrdb.pl: Permission denied at Makefile.PL
line 118
cannot restore permissions to 0100555 for scripts_temp/bp_nrdb.pl: Permission de
nied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_heterogeneity_test.pl: Permission denied
at Makefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_heterogeneity_test.pl:
Permission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_chaos_plot.pl: Permission denied at Makef
ile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_chaos_plot.pl: Permiss
ion denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_oligo_count.pl: Permission denied at Make
file.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_oligo_count.pl: Permis
sion denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_blast2tree.pl: Permission denied at Makef
ile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_blast2tree.pl: Permiss
ion denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_biofetch_genbank_proxy.pl: Permission den
ied at Makefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_biofetch_genbank_proxy
.pl: Permission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_search2alnblocks.pl: Permission denied at
Makefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_search2alnblocks.pl: P
ermission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_search2tribe.pl: Permission denied at Mak
efile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_search2tribe.pl: Permi
ssion denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_seqconvert.pl: Permission denied at Makef
ile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_seqconvert.pl: Permiss
ion denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_mask_by_search.pl: Permission denied at M
akefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_mask_by_search.pl: Per
mission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_sreformat.pl: Permission denied at Makefi
le.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_sreformat.pl: Permissi
on denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_seq_length.pl: Permission denied at Makef
ile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_seq_length.pl: Permiss
ion denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_extract_feature_seq.pl: Permission denied
at Makefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_extract_feature_seq.pl
: Permission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_split_seq.pl: Permission denied at Makefi
le.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_split_seq.pl: Permissi
on denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_mrtrans.pl: Permission denied at Makefile
.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_mrtrans.pl: Permission
denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_aacomp.pl: Permission denied at Makefile.
PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_aacomp.pl: Permission
denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_remote_blast.pl: Permission denied at Mak
efile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_remote_blast.pl: Permi
ssion denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_flanks.pl: Permission denied at Makefile.
PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_flanks.pl: Permission
denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_genbank2gff.pl: Permission denied at Make
file.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_genbank2gff.pl: Permis
sion denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_process_sgd.pl: Permission denied at Make
file.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_process_sgd.pl: Permis
sion denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_process_wormbase.pl: Permission denied at
Makefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_process_wormbase.pl: P
ermission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_gccalc.pl: Permission denied at Makefile.
PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_gccalc.pl: Permission
denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_generate_histogram.pl: Permission denied
at Makefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_generate_histogram.pl:
Permission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_fast_load_gff.pl: Permission denied at Ma
kefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_fast_load_gff.pl: Perm
ission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_local_taxonomydb_query.pl: Permission den
ied at Makefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_local_taxonomydb_query
.pl: Permission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_process_ncbi_human.pl: Permission denied
at Makefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_process_ncbi_human.pl:
Permission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_load_gff.pl: Permission denied at Makefil
e.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_load_gff.pl: Permissio
n denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_biogetseq.pl: Permission denied at Makefi
le.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_biogetseq.pl: Permissi
on denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_feature_draw.pl: Permission denied at Mak
efile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_feature_draw.pl: Permi
ssion denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_search2gff.pl: Permission denied at Makef
ile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_search2gff.pl: Permiss
ion denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_search_overview.pl: Permission denied at
Makefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_search_overview.pl: Pe
rmission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_bulk_load_gff.pl: Permission denied at Ma
kefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_bulk_load_gff.pl: Perm
ission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_frend.pl: Permission denied at Makefile.P
L line 118
cannot restore permissions to 0100555 for scripts_temp/bp_frend.pl: Permission d
enied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_translate_seq.pl: Permission denied at Ma
kefile.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_translate_seq.pl: Perm
ission denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_fetch.pl: Permission denied at Makefile.P
L line 118
cannot restore permissions to 0100555 for scripts_temp/bp_fetch.pl: Permission d
enied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_search2BSML.pl: Permission denied at Make
file.PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_search2BSML.pl: Permis
sion denied at Makefile.PL line 118
cannot unlink file for scripts_temp/bp_biblio.pl: Permission denied at Makefile.
PL line 118
cannot restore permissions to 0100555 for scripts_temp/bp_biblio.pl: Permission
denied at Makefile.PL line 118
cannot remove directory for ./scripts_temp: Directory not empty at Makefile.PL l
ine 118
cannot restore permissions to 0755 for ./scripts_temp: Operation not permitted a
t Makefile.PL line 118
External Module GD::SVG, Generate optional SVG output,
is not installed on this computer.
The in Bioperl needs it for Bio::Graphics
External Module Ace, Aceperl,
is not installed on this computer.
The Bio::DB::Ace in Bioperl needs it for access of ACeDB database
External Module SOAP::Lite, SOAP protocol,
is not installed on this computer.
The Bio::DB::XEMBLService in Bioperl needs it for XEMBL Services (also Bibliog
raphic queries in Biblio::)
External Module GD, Graphical Drawing Toolkit,
is not installed on this computer.
The Bio::Graphics in Bioperl needs it for Rendering Sequences and Features
External Module XML::Twig, Available on CPAN,
is not installed on this computer.
The Module Bio::Variation::IO::xml.pm in Bioperl needs it for parsing of XML d
ocuments
External Module SVG, Generate optional SVG output,
is not installed on this computer.
The in Bioperl needs it for Bio::Graphics
External Module Text::Shellwords, Execute shell commands,
is not installed on this computer.
The Bio::Graphics in Bioperl needs it for test scripts
External Module XML::Parser::PerlSAX, Parsing of XML documents,
is not installed on this computer.
The Bio::SeqIO::game,Bio::Variation::* in Bioperl needs it for Bio::Variation
code, GAME parser
External Module DBD::mysql, Mysql driver,
is not installed on this computer.
The Bio::DB::GFF in Bioperl needs it for loading and querying of Mysql-based G
FF feature databases
External Module Graph::Directed, Generic Graph data stucture and algorithms,
is not installed on this computer.
The Bio::Ontology::SimpleOntologyEngine in Bioperl needs it for Ontology Engin
e implementation for the GO parser
Information:
There are some external packages and perl modules, listed above, which
bioperl uses. This only effects the functionality which is listed above:
the rest of bioperl will work fine, which includes nearly all of the
core packages.
The installation of these external packages is very simple. You
can read more about bioperl external dependencies in the INSTALL
file or at:
http://bioperl.org/Core/Latest/INSTALL
Enjoy the rest of bioperl, which you can use after going 'make install'
Writing Makefile for Bio
shafiq at linux-22nr:~/source/bio> make
shafiq at linux-22nr:~/source/bio> make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/AAChange...................ok
t/AAReverseMutate............ok
t/AlignIO....................ok
t/AlignStats.................ok
t/Allele.....................ok
t/Alphabet...................ok
t/Annotation.................Useless localization of scalar assignment at /home/
shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/Annotation.................ok
t/AnnotationAdaptor..........ok
t/Assembly...................ok
t/Biblio.....................SOAP::Lite not installed. Skipping some tests.
t/Biblio.....................ok
1/24 skipped: various reasons
t/Biblio_biofetch............ok
t/BiblioReferences...........ok
t/BioDBGFF...................ok
t/BioFetch_DB................FAILED tests 8, 20-21, 27
Failed 4/27 tests, 85.19% okay
t/BioGraphics................GD or Text::Shellwords modules are not installed. T
his means that Bio::Graphics module is unusable. Skipping tests.
t/BioGraphics................ok
t/BlastIndex.................ok
t/BPbl2seq...................ok
t/BPlite.....................ok
t/BPpsilite..................ok
t/Chain......................ok
t/cigarstring................ok
t/ClusterIO..................XML::Parser::PerlSAX not loaded. This means Cluster
IO::dbsnp test cannot be executed. Skipping
t/ClusterIO..................ok
t/Coalescent.................ok
t/CodonTable.................ok
t/consed.....................ok
t/CoordinateGraph............ok
t/CoordinateMapper...........ok
t/Correlate..................Useless localization of scalar assignment at /home/
shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/Correlate..................ok
t/CytoMap....................ok
t/DB.........................FAILED tests 30-31
Failed 2/78 tests, 97.44% okay (less 1 skipped test: 75 okay, 96.15%)
t/DBCUTG.....................ok
t/DBFasta....................ok
t/DNAMutation................ok
t/Domcut.....................ok
t/ECnumber...................Useless localization of scalar assignment at /home/
shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/ECnumber...................ok
t/ELM........................ok 1/14
-------------------- WARNING ---------------------
MSG: Bio::Tools::Analysis::Protein::ELM Request Error:
400 URL must be absolute
Content-Type: text/plain
Client-Date: Wed, 26 Nov 2008 13:50:44 GMT
Client-Warning: Internal response
400 URL must be absolute
---------------------------------------------------
t/ELM........................ok
t/EMBL_DB....................FAILED tests 6, 13-14
Failed 3/15 tests, 80.00% okay
t/EMBOSS_Tools...............ok
t/EncodedSeq.................ok
t/ePCR.......................ok
t/ESEfinder..................ok
t/est2genome.................ok
t/Exception..................ok
t/Exonerate..................ok
t/flat.......................ok
t/FootPrinter................ok
t/game.......................XML::Parser::PerlSAX not loaded. This means game te
st cannot be executed. Skipping
t/game.......................ok
t/GDB........................ok
t/GeneCoordinateMapper.......ok 1/113
-------------------- WARNING ---------------------
MSG: sorted sublocation array requested but root location doesn't define seq_id
(at least one sublocation does!)
---------------------------------------------------
-------------------- WARNING ---------------------
MSG: sorted sublocation array requested but root location doesn't define seq_id
(at least one sublocation does!)
---------------------------------------------------
t/GeneCoordinateMapper.......ok 83/113Use of uninitialized value in concatenatio
n (.) or string at /home/shafiq/source/bio/blib/lib/Bio/Coordinate/GeneMapper.pm
line 814.
t/GeneCoordinateMapper.......ok
t/Geneid.....................ok
t/Genewise...................ok
2/51 skipped: various reasons
t/Genomewise.................ok
t/Genpred....................ok
t/GFF........................ok 1/32Filehandle GEN0 opened only for output at /h
ome/shafiq/source/bio/blib/lib/Bio/Root/IO.pm line 440.
Filehandle GEN1 opened only for output at /home/shafiq/source/bio/blib/lib/Bio/R
oot/IO.pm line 440.
t/GFF........................ok
t/GOR4.......................ok
t/GOterm.....................Useless localization of scalar assignment at /home/
shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/GOterm.....................ok
t/GuessSeqFormat.............ok 1/46Bio::SeqIO: game cannot be found
Exception
------------- EXCEPTION -------------
MSG: Failed to load module Bio::SeqIO::game. Can't locate XML/Parser/PerlSAX.pm
in @INC (@INC contains: t .. /home/shafiq/source/bio/blib/lib /home/shafiq/sourc
e/bio/blib/arch /usr/lib/perl5/5.10.0/i586-linux-thread-multi /usr/lib/perl5/5.1
0.0 /usr/lib/perl5/site_perl/5.10.0/i586-linux-thread-multi /usr/lib/perl5/site_
perl/5.10.0 /usr/lib/perl5/vendor_perl/5.10.0/i586-linux-thread-multi /usr/lib/p
erl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl .) at /home/shafiq/source/bio
/blib/lib/Bio/SeqIO/game/gameSubs.pm line 70.
BEGIN failed--compilation aborted at /home/shafiq/source/bio/blib/lib/Bio/SeqIO/
game/gameSubs.pm line 70.
Compilation failed in require at /home/shafiq/source/bio/blib/lib/Bio/SeqIO/game
/gameHandler.pm line 62.
BEGIN failed--compilation aborted at /home/shafiq/source/bio/blib/lib/Bio/SeqIO/
game/gameHandler.pm line 62.
Compilation failed in require at /home/shafiq/source/bio/blib/lib/Bio/SeqIO/game
.pm line 76.
BEGIN failed--compilation aborted at /home/shafiq/source/bio/blib/lib/Bio/SeqIO/
game.pm line 76.
Compilation failed in require at /home/shafiq/source/bio/blib/lib/Bio/Root/Root.
pm line 394.
STACK Bio::Root::Root::_load_module /home/shafiq/source/bio/blib/lib/Bio/Root/Ro
ot.pm:396
STACK (eval) /home/shafiq/source/bio/blib/lib/Bio/SeqIO.pm:549
STACK Bio::SeqIO::_load_format_module /home/shafiq/source/bio/blib/lib/Bio/SeqIO
.pm:548
STACK Bio::SeqIO::new /home/shafiq/source/bio/blib/lib/Bio/SeqIO.pm:377
STACK (eval) t/GuessSeqFormat.t:61
STACK toplevel t/GuessSeqFormat.t:60
--------------------------------------
For more information about the SeqIO system please see the SeqIO docs.
This includes ways of checking for formats at compile time, not run time
t/GuessSeqFormat.............FAILED test 11
Failed 1/46 tests, 97.83% okay
t/hmmer......................ok
t/HNN........................ok
t/Index......................ok
t/InstanceSite...............ok
t/InterProParser.............ok 1/47Bio::OntologyIO: InterProParser cannot be fo
und
Exception
------------- EXCEPTION -------------
MSG: Failed to load module Bio::OntologyIO::InterProParser. Can't locate XML/Par
ser/PerlSAX.pm in @INC (@INC contains: t .. . ./blib/lib /home/shafiq/source/bio
/blib/lib /home/shafiq/source/bio/blib/arch /usr/lib/perl5/5.10.0/i586-linux-thr
ead-multi /usr/lib/perl5/5.10.0 /usr/lib/perl5/site_perl/5.10.0/i586-linux-threa
d-multi /usr/lib/perl5/site_perl/5.10.0 /usr/lib/perl5/vendor_perl/5.10.0/i586-l
inux-thread-multi /usr/lib/perl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl)
at Bio/OntologyIO/InterProParser.pm line 84.
BEGIN failed--compilation aborted at Bio/OntologyIO/InterProParser.pm line 84.
Compilation failed in require at Bio/Root/Root.pm line 394.
STACK Bio::Root::Root::_load_module Bio/Root/Root.pm:396
STACK (eval) Bio/OntologyIO.pm:255
STACK Bio::OntologyIO::_load_format_module Bio/OntologyIO.pm:254
STACK Bio::OntologyIO::new Bio/OntologyIO.pm:165
STACK toplevel t/InterProParser.t:52
--------------------------------------
For more information about the OntologyIO system please see the docs.
This includes ways of checking for formats at compile time, not run time
t/InterProParser.............NOK 2/47Can't call method "next_ontology" on an und
efined value at t/InterProParser.t line 59.
t/InterProParser.............dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED test 2
Failed 1/47 tests, 97.87% okay
t/IUPAC......................ok
t/largefasta.................ok
t/largepseq..................ok
t/LinkageMap.................ok
t/LiveSeq....................ok
t/LocatableSeq...............ok
t/Location...................ok
t/LocationFactory............ok
t/LocusLink..................ok 1/23Useless localization of scalar assignment at
/home/shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/LocusLink..................ok
t/lucy.......................ok
t/Map........................ok
t/MapIO......................ok
t/Matrix.....................ok
t/Measure....................Useless localization of scalar assignment at /home/
shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/Measure....................ok
t/MeSH.......................ok
t/MetaSeq....................ok
t/MicrosatelliteMarker.......ok
t/MiniMIMentry...............Useless localization of scalar assignment at /home/
shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/MiniMIMentry...............ok
t/MitoProt...................ok
t/Molphy.....................ok
t/multiple_fasta.............ok
t/Mutation...................ok
t/Mutator....................ok
t/NetPhos....................ok
t/Node.......................ok
t/OddCodes...................ok
t/OMIMentry..................Useless localization of scalar assignment at /home/
shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/OMIMentry..................ok
t/OMIMentryAllelicVariant....Useless localization of scalar assignment at /home/
shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/OMIMentryAllelicVariant....ok
t/OMIMparser.................Useless localization of scalar assignment at /home/
shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/OMIMparser.................ok
t/Ontology...................
Graph.pm doesn't seem to be installed on this system -- the GO Parser needs it..
.
t/Ontology...................ok
t/OntologyEngine.............Useless localization of scalar assignment at /home/
shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/OntologyEngine.............ok
t/PAML.......................ok
t/Perl.......................ok 1/14Use of uninitialized value $au in substituti
on (s///) at /home/shafiq/source/bio/blib/lib/Bio/SeqIO/swiss.pm line 855, <STRE
AM> line 45.
t/Perl.......................ok
t/phd........................ok
t/Phenotype..................Useless localization of scalar assignment at /home/
shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/Phenotype..................ok
t/PhylipDist.................ok
t/pICalculator...............ok
t/Pictogram..................SVG not installed, skipping tests at t/Pictogram.t
line 29.
t/Pictogram..................ok
t/PopGen.....................ok
t/PopGenSims.................ok
t/primaryqual................ok
t/PrimarySeq.................ok
t/primedseq..................ok
t/Primer.....................ok
t/primer3....................ok
t/Promoterwise...............ok
t/ProtDist...................ok
t/psm........................ok
t/QRNA.......................ok
t/qual.......................ok
t/RandDistFunctions..........ok
t/RandomTreeFactory..........ok
t/Range......................ok
t/RangeI.....................ok
t/RefSeq.....................ok
t/Registry...................DB_File and BerkeleyDB not found. Skipping DB_File
tests
t/Registry...................ok
t/Relationship...............Useless localization of scalar assignment at /home/
shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/Relationship...............ok
t/RelationshipType...........Useless localization of scalar assignment at /home/
shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/RelationshipType...........ok
t/RemoteBlast................ok
4/6 skipped: various reasons
t/RepeatMasker...............ok
t/RestrictionAnalysis........ok
t/RestrictionEnzyme..........ok
t/RestrictionIO..............ok 1/14
------------- EXCEPTION -------------
MSG: Could not open >/tmp/r: Permission denied
STACK Bio::Root::IO::_initialize_io /home/shafiq/source/bio/blib/lib/Bio/Root/IO
.pm:273
STACK Bio::SeqIO::_initialize /home/shafiq/source/bio/blib/lib/Bio/SeqIO.pm:447
STACK Bio::Restriction::IO::base::_initialize /home/shafiq/source/bio/blib/lib/B
io/Restriction/IO/base.pm:87
STACK Bio::Restriction::IO::base::new /home/shafiq/source/bio/blib/lib/Bio/Restr
iction/IO/base.pm:81
STACK Bio::Restriction::IO::new /home/shafiq/source/bio/blib/lib/Bio/Restriction
/IO.pm:152
STACK toplevel t/RestrictionIO.t:49
--------------------------------------
t/RestrictionIO..............dubious
Test returned status 13 (wstat 3328, 0xd00)
DIED. FAILED tests 7-14
Failed 8/14 tests, 42.86% okay
t/RNAChange..................ok
t/RootI......................ok
t/RootIO.....................ok
t/RootStorable...............ok
t/Scansite...................ok
t/scf........................ok
t/SearchDist.................ok
t/SearchIO...................XML::Parser::PerlSAX or HTML::Entities not loaded.
This means SearchIO::blastxml test cannot be executed. Skipping
t/SearchIO...................ok
t/Seq........................ok
t/SeqAnalysisParser..........ok
t/SeqBuilder.................ok
t/SeqDiff....................ok
t/SeqFeatCollection..........ok
t/SeqFeature.................Useless localization of scalar assignment at /home/
shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/SeqFeature.................ok
t/seqfeaturePrimer...........ok
t/SeqIO......................ok
3/235 skipped: various reasons
t/SeqPattern.................ok
t/SeqStats...................ok
t/SequenceFamily.............ok
t/sequencetrace..............ok
t/SeqUtils...................ok
t/seqwithquality.............ok
t/SeqWords...................ok
t/Sigcleave..................ok
t/Sim4.......................ok
t/SimilarityPair.............ok
t/SimpleAlign................ok
t/simpleGOparser.............
Graph.pm doesn't seem to be installed on this system -- the GO Parser needs it..
.
t/simpleGOparser.............ok
t/sirna......................ok
t/SiteMatrix.................ok
t/SNP........................ok
t/Sopma......................ok
t/Species....................ok
t/splicedseq.................ok
t/StandAloneBlast............ok
t/StructIO...................ok
t/Structure..................ok
t/Swiss......................ok 1/5
------------- EXCEPTION -------------
MSG: Could not open >test.swiss: Permission denied
STACK Bio::Root::IO::_initialize_io /home/shafiq/source/bio/blib/lib/Bio/Root/IO
.pm:273
STACK Bio::SeqIO::_initialize /home/shafiq/source/bio/blib/lib/Bio/SeqIO.pm:447
STACK Bio::SeqIO::swiss::_initialize /home/shafiq/source/bio/blib/lib/Bio/SeqIO/
swiss.pm:131
STACK Bio::SeqIO::new /home/shafiq/source/bio/blib/lib/Bio/SeqIO.pm:358
STACK Bio::SeqIO::new /home/shafiq/source/bio/blib/lib/Bio/SeqIO.pm:378
STACK toplevel t/Swiss.t:49
--------------------------------------
t/Swiss......................dubious
Test returned status 13 (wstat 3328, 0xd00)
DIED. FAILED tests 3-5
Failed 3/5 tests, 40.00% okay
t/Symbol.....................ok
t/Taxonomy...................ok
t/Tempfile...................ok
t/Term.......................Useless localization of scalar assignment at /home/
shafiq/source/bio/blib/lib/Bio/Root/Object.pm line 699.
t/Term.......................ok
t/Tools......................ok
t/Tree.......................ok
t/TreeIO.....................ok
t/trim.......................ok
t/tutorial...................ok 3/21Use of uninitialized value $au in substituti
on (s///) at Bio/SeqIO/swiss.pm line 855, <STREAM> line 45.
t/tutorial...................ok 17/21Bio::SeqIO: game cannot be found
Exception
------------- EXCEPTION -------------
MSG: Failed to load module Bio::SeqIO::game. Can't locate XML/Parser/PerlSAX.pm
in @INC (@INC contains: . t /home/shafiq/source/bio/blib/lib /home/shafiq/source
/bio/blib/arch /usr/lib/perl5/5.10.0/i586-linux-thread-multi /usr/lib/perl5/5.10
.0 /usr/lib/perl5/site_perl/5.10.0/i586-linux-thread-multi /usr/lib/perl5/site_p
erl/5.10.0 /usr/lib/perl5/vendor_perl/5.10.0/i586-linux-thread-multi /usr/lib/pe
rl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl) at Bio/SeqIO/game/gameSubs.pm
line 70.
BEGIN failed--compilation aborted at Bio/SeqIO/game/gameSubs.pm line 70.
Compilation failed in require at Bio/SeqIO/game/gameHandler.pm line 62.
BEGIN failed--compilation aborted at Bio/SeqIO/game/gameHandler.pm line 62.
Compilation failed in require at Bio/SeqIO/game.pm line 76.
BEGIN failed--compilation aborted at Bio/SeqIO/game.pm line 76.
Compilation failed in require at /home/shafiq/source/bio/blib/lib/Bio/Root/Root.
pm line 394.
STACK Bio::Root::Root::_load_module /home/shafiq/source/bio/blib/lib/Bio/Root/Ro
ot.pm:396
STACK (eval) /home/shafiq/source/bio/blib/lib/Bio/SeqIO.pm:549
STACK Bio::SeqIO::_load_format_module /home/shafiq/source/bio/blib/lib/Bio/SeqIO
.pm:548
STACK Bio::SeqIO::new /home/shafiq/source/bio/blib/lib/Bio/SeqIO.pm:377
STACK (eval) /home/shafiq/source/bio/blib/lib/bptutorial.pl:4027
STACK main::__ANON__ /home/shafiq/source/bio/blib/lib/bptutorial.pl:4025
STACK main::run_examples /home/shafiq/source/bio/blib/lib/bptutorial.pl:4152
STACK toplevel t/tutorial.t:23
--------------------------------------
For more information about the SeqIO system please see the SeqIO docs.
This includes ways of checking for formats at compile time, not run time
Can't call method "next_seq" on an undefined value at /home/shafiq/source/bio/bl
ib/lib/bptutorial.pl line 4035.
t/tutorial...................dubious
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 19-21
Failed 3/21 tests, 85.71% okay
t/UCSCParsers................ok
t/Unflattener................ok
t/Unflattener2...............ok
t/UniGene....................ok
t/Variation_IO...............ok 3/25
The XML-format conversion requires the CPAN modules XML::Twig,
XML::Writer, and
IO::String to be installed on your system, which they probably aren't.
Skipping these
tests.
t/Variation_IO...............ok
t/WABA.......................ok
t/XEMBL_DB...................SOAP::Lite and/or XML::DOM not installed.
This mean s that
Bio::DB::XEMBL module is not usable. Skipping tests.
t/XEMBL_DB...................ok
Failed Test Stat Wstat Total Fail List of Failed
-------------------------------------------------------------------------------
t/BioFetch_DB.t 27 4 8 20-21 27
t/DB.t 78 2 30-31
t/EMBL_DB.t 15 3 6 13-14
t/GuessSeqFormat.t 46 1 11
t/InterProParser.t 2 512 47 1 2
t/RestrictionIO.t 13 3328 14 16 7-14
t/Swiss.t 13 3328 5 6 3-5
t/tutorial.t 2 512 21 6 19-21
11 subtests skipped.
Failed 8/179 test scripts. 25/8122 subtests failed.
Files=179, Tests=8122, 119 wallclock secs (67.10 cusr + 3.36 csys = 70.46 CPU)
Failed 8/179 test programs. 25/8122 subtests failed.
make: *** [test_dynamic] Error 255
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