[Bioperl-l] installing bioperl
Warren W. Kretzschmar
wkretzsch at gmail.com
Fri Jul 30 15:37:08 UTC 2010
Alternatively I think you might have run "make install" when what you
actually wanted to run was "sudo make install". The sudo means you
install everything with root rights (which you say you have). It'll
ask you for a password and then it will have the rights to install
into /usr/local/bin
Cheers,
Warren
On Fri, Jul 30, 2010 at 9:54 AM, Robson de Souza <robfsouza at gmail.com> wrote:
> Did you try, as root,
>
> ./Build.pl --install_base /opt/local
>
> ?
>
> Also, check the INSTALL file at the root of the bioperl distribution.
> Robson
>
> On Fri, Jul 30, 2010 at 5:37 AM, Carrie O'Malley <com505 at york.ac.uk> wrote:
>> Hi there
>> I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too.
>> I am not able to complete the installation as every time I get:
>>
>> Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1
>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>> ERROR: Can't create '/usr/local/bin'
>> mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479
>>
>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>> at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902
>>
>>
>> I have tried using both methods to install into a local folder and get the same thing
>>
>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>> ERROR: Can't create '/home/users/carrieomalley/bin'
>> mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479
>>
>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>> at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902
>>
>> I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated.
>>
>>
>> If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :(
>>
>>
>> Many thanks in advance
>> Carrie
>>
>>
>>
>>
>>
>> Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0
>> Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL
>> Checking whether your kit is complete...
>> Looks good
>>
>> Checking prerequisites...
>> - ERROR: Data::Stag is not installed
>> (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand)
>> CPAN: Storable loaded ok (v2.18)
>> Going to read /Users/carrieomalley/.cpan/Metadata
>> Database was generated on Sat, 10 Jul 2010 11:27:04 GMT
>> Running install for module 'Data::Stag'
>> 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs'
>> Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz
>> CPAN: Digest::SHA loaded ok (v5.45)
>> CPAN: Compress::Zlib loaded ok (v2.008)
>> Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok
>> x Data-Stag-0.11/
>> x Data-Stag-0.11/c-ext/
>> x Data-Stag-0.11/c-ext/README.c-ext
>> x Data-Stag-0.11/c-ext/staglib.c
>> x Data-Stag-0.11/c-ext/staglib.h
>> x Data-Stag-0.11/Changes
>> x Data-Stag-0.11/Data/
>> x Data-Stag-0.11/Data/Stag/
>> x Data-Stag-0.11/Data/Stag/Arr2HTML.pm
>> x Data-Stag-0.11/Data/Stag/Base.pm
>> x Data-Stag-0.11/Data/Stag/BaseGenerator.pm
>> x Data-Stag-0.11/Data/Stag/BaseHandler.pm
>> x Data-Stag-0.11/Data/Stag/ChainHandler.pm
>> x Data-Stag-0.11/Data/Stag/DTDWriter.pm
>> x Data-Stag-0.11/Data/Stag/GraphHandler.pm
>> x Data-Stag-0.11/Data/Stag/HashDB.pm
>> x Data-Stag-0.11/Data/Stag/IndentParser.pm
>> x Data-Stag-0.11/Data/Stag/IndentWriter.pm
>> x Data-Stag-0.11/Data/Stag/ITextParser.pm
>> x Data-Stag-0.11/Data/Stag/ITextWriter.pm
>> x Data-Stag-0.11/Data/Stag/null.pm
>> x Data-Stag-0.11/Data/Stag/PerlWriter.pm
>> x Data-Stag-0.11/Data/Stag/PodParser.pm
>> x Data-Stag-0.11/Data/Stag/SAX2Stag.pm
>> x Data-Stag-0.11/Data/Stag/Simple.pm
>> x Data-Stag-0.11/Data/Stag/StagDB.pm
>> x Data-Stag-0.11/Data/Stag/StagI.pm
>> x Data-Stag-0.11/Data/Stag/StagImpl.pm
>> x Data-Stag-0.11/Data/Stag/SxprParser.pm
>> x Data-Stag-0.11/Data/Stag/SxprWriter.pm
>> x Data-Stag-0.11/Data/Stag/Util.pm
>> x Data-Stag-0.11/Data/Stag/Writer.pm
>> x Data-Stag-0.11/Data/Stag/XMLParser.pm
>> x Data-Stag-0.11/Data/Stag/XMLWriter.pm
>> x Data-Stag-0.11/Data/Stag/XSLHandler.pm
>> x Data-Stag-0.11/Data/Stag/XSLTHandler.pm
>> x Data-Stag-0.11/Data/Stag.pm
>> x Data-Stag-0.11/dev/
>> x Data-Stag-0.11/dev/create-manifest.sh
>> x Data-Stag-0.11/dev/data-stag.spec
>> x Data-Stag-0.11/dev/mkspec.pl
>> x Data-Stag-0.11/elisp/
>> x Data-Stag-0.11/elisp/itext-mode.el
>> x Data-Stag-0.11/homepage/
>> x Data-Stag-0.11/homepage/archBIG.png
>> x Data-Stag-0.11/homepage/dbstag-tutorial.sgml
>> x Data-Stag-0.11/homepage/images/
>> x Data-Stag-0.11/homepage/images/k-schema-diagram.png
>> x Data-Stag-0.11/homepage/images/rr-schema-diagram.png
>> x Data-Stag-0.11/homepage/index.html
>> x Data-Stag-0.11/homepage/makefile
>> x Data-Stag-0.11/homepage/mk.sh
>> x Data-Stag-0.11/homepage/mkpodhtml.pl
>> x Data-Stag-0.11/homepage/mkscriptdoc.pl
>> x Data-Stag-0.11/homepage/script-docs/
>> x Data-Stag-0.11/homepage/script-docs/selectall_html.html
>> x Data-Stag-0.11/homepage/script-docs/selectall_xml.html
>> x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html
>> x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html
>> x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html
>> x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html
>> x Data-Stag-0.11/homepage/script-docs/stag-db.html
>> x Data-Stag-0.11/homepage/script-docs/stag-diff.html
>> x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html
>> x Data-Stag-0.11/homepage/script-docs/stag-elcount.html
>> x Data-Stag-0.11/homepage/script-docs/stag-eval.html
>> x Data-Stag-0.11/homepage/script-docs/stag-filter.html
>> x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html
>> x Data-Stag-0.11/homepage/script-docs/stag-flatten.html
>> x Data-Stag-0.11/homepage/script-docs/stag-grep.html
>> x Data-Stag-0.11/homepage/script-docs/stag-handle.html
>> x Data-Stag-0.11/homepage/script-docs/stag-ir.html
>> x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html
>> x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html
>> x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html
>> x Data-Stag-0.11/homepage/script-docs/stag-join.html
>> x Data-Stag-0.11/homepage/script-docs/stag-merge.html
>> x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html
>> x Data-Stag-0.11/homepage/script-docs/stag-parse.html
>> x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html
>> x Data-Stag-0.11/homepage/script-docs/stag-query.html
>> x Data-Stag-0.11/homepage/script-docs/stag-show-template.html
>> x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html
>> x Data-Stag-0.11/homepage/script-docs/stag-splitter.html
>> x Data-Stag-0.11/homepage/script-docs/stag-storenode.html
>> x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html
>> x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html
>> x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html
>> x Data-Stag-0.11/homepage/script-docs/stag-view.html
>> x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html
>> x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html
>> x Data-Stag-0.11/homepage/script-list.html
>> x Data-Stag-0.11/homepage/stag-db-tutorial.html
>> x Data-Stag-0.11/homepage/stag-poster.html
>> x Data-Stag-0.11/INSTALL
>> x Data-Stag-0.11/Makefile.PL
>> x Data-Stag-0.11/MANIFEST
>> x Data-Stag-0.11/META.yml
>> x Data-Stag-0.11/README
>> x Data-Stag-0.11/scripts/
>> x Data-Stag-0.11/scripts/stag-autoschema.pl
>> x Data-Stag-0.11/scripts/stag-db.pl
>> x Data-Stag-0.11/scripts/stag-diff.pl
>> x Data-Stag-0.11/scripts/stag-drawtree.pl
>> x Data-Stag-0.11/scripts/stag-elcount.pl
>> x Data-Stag-0.11/scripts/stag-eval.pl
>> x Data-Stag-0.11/scripts/stag-filter.pl
>> x Data-Stag-0.11/scripts/stag-findsubtree.pl
>> x Data-Stag-0.11/scripts/stag-flatten.pl
>> x Data-Stag-0.11/scripts/stag-grep.pl
>> x Data-Stag-0.11/scripts/stag-handle.pl
>> x Data-Stag-0.11/scripts/stag-itext2simple.pl
>> x Data-Stag-0.11/scripts/stag-itext2sxpr.pl
>> x Data-Stag-0.11/scripts/stag-itext2xml.pl
>> x Data-Stag-0.11/scripts/stag-join.pl
>> x Data-Stag-0.11/scripts/stag-merge.pl
>> x Data-Stag-0.11/scripts/stag-mogrify.pl
>> x Data-Stag-0.11/scripts/stag-parse.pl
>> x Data-Stag-0.11/scripts/stag-query.pl
>> x Data-Stag-0.11/scripts/stag-splitter.pl
>> x Data-Stag-0.11/scripts/stag-view.pl
>> x Data-Stag-0.11/scripts/stag-xml2itext.pl
>> x Data-Stag-0.11/scripts/stag-xmlsplit.pl
>> x Data-Stag-0.11/t/
>> x Data-Stag-0.11/t/animal.x
>> x Data-Stag-0.11/t/autoschema.t
>> x Data-Stag-0.11/t/barfly.x
>> x Data-Stag-0.11/t/bio.x
>> x Data-Stag-0.11/t/chainhandler.t
>> x Data-Stag-0.11/t/collapse.x
>> x Data-Stag-0.11/t/data/
>> x Data-Stag-0.11/t/data/attrs.xml
>> x Data-Stag-0.11/t/data/bf.txt
>> x Data-Stag-0.11/t/data/eco.el
>> x Data-Stag-0.11/t/data/eco.itext
>> x Data-Stag-0.11/t/data/homol.itext
>> x Data-Stag-0.11/t/data/persons.el
>> x Data-Stag-0.11/t/db.t
>> x Data-Stag-0.11/t/emptytag.t
>> x Data-Stag-0.11/t/get.t
>> x Data-Stag-0.11/t/graph.x
>> x Data-Stag-0.11/t/handlers.t
>> x Data-Stag-0.11/t/handlers2.t
>> x Data-Stag-0.11/t/handlers2.x
>> x Data-Stag-0.11/t/hashdb.t
>> x Data-Stag-0.11/t/hashdb.x
>> x Data-Stag-0.11/t/homol.t
>> x Data-Stag-0.11/t/lisp.x
>> x Data-Stag-0.11/t/parsestr.t
>> x Data-Stag-0.11/t/path.x
>> x Data-Stag-0.11/t/path2.x
>> x Data-Stag-0.11/t/qmatch.t
>> x Data-Stag-0.11/t/roundtrip-attrs.t
>> x Data-Stag-0.11/t/set-attrs.t
>> x Data-Stag-0.11/t/set.t
>> x Data-Stag-0.11/t/sxpr.t
>> x Data-Stag-0.11/t/unhash.t
>> x Data-Stag-0.11/t/unset.t
>> x Data-Stag-0.11/t/write.t
>> x Data-Stag-0.11/t/xml1.t
>> x Data-Stag-0.11/t/xml2.t
>> CPAN: File::Temp loaded ok (v0.18)
>> Warning (usually harmless): 'YAML' not installed, will not store persistent state
>>
>> CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz
>>
>>
>> External Module XML::LibXSLT, XSLT,
>> is not installed on this computer.
>> Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations
>>
>> External Module XML::Parser::PerlSAX, SAX Handler,
>> is not installed on this computer.
>> Data::Stag::XMLParser in Data::Stag needs it for parsing XML
>>
>> External Module GD, Graphical Drawing Toolkit,
>> is not installed on this computer.
>> stag-drawtree.pl in Data::Stag needs it for drawing trees
>>
>> External Module Graph::Directed, Generic Graph data stucture and algorithms,
>> is not installed on this computer.
>> Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs
>>
>> External Module Tk, Tk,
>> is not installed on this computer.
>> stag-view.pl in Data::Stag needs it for tree viewer
>>
>>
>> Information:
>>
>> There are some external packages and perl modules, listed above, which
>> stag uses. This only effects the functionality which is listed above:
>> the rest of stag will work fine, which includes nearly all of the
>> core functionality.
>>
>> Enjoy the rest of stag, which you can use after going 'make install'
>>
>> Checking if your kit is complete...
>> Looks good
>> Writing Makefile for Data
>> Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites
>> cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm
>> cp Data/Stag.pm blib/lib/Data/Stag.pm
>> cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm
>> cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm
>> cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm
>> cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm
>> cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm
>> cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm
>> cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm
>> cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm
>> cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm
>> cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm
>> cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm
>> cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm
>> cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm
>> cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm
>> cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm
>> cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm
>> cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm
>> cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm
>> cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm
>> cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm
>> cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm
>> cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm
>> cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm
>> cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm
>> cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm
>> cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm
>> cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm
>> cp scripts/stag-view.pl blib/script/stag-view.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl
>> cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl
>> cp scripts/stag-grep.pl blib/script/stag-grep.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl
>> cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl
>> cp scripts/stag-merge.pl blib/script/stag-merge.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl
>> cp scripts/stag-parse.pl blib/script/stag-parse.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl
>> cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl
>> cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl
>> cp scripts/stag-join.pl blib/script/stag-join.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl
>> cp scripts/stag-db.pl blib/script/stag-db.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl
>> cp scripts/stag-filter.pl blib/script/stag-filter.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl
>> cp scripts/stag-handle.pl blib/script/stag-handle.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl
>> cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl
>> cp scripts/stag-query.pl blib/script/stag-query.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl
>> cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl
>> cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl
>> cp scripts/stag-flatten.pl blib/script/stag-flatten.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl
>> cp scripts/stag-splitter.pl blib/script/stag-splitter.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl
>> cp scripts/stag-diff.pl blib/script/stag-diff.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl
>> cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl
>> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl
>> Manifying blib/man1/stag-view.pl.1
>> Manifying blib/man1/stag-mogrify.pl.1
>> Manifying blib/man1/stag-grep.pl.1
>> Manifying blib/man1/stag-handle.pl.1
>> Manifying blib/man1/stag-drawtree.pl.1
>> Manifying blib/man1/stag-query.pl.1
>> Manifying blib/man1/stag-merge.pl.1
>> Manifying blib/man1/stag-parse.pl.1
>> Manifying blib/man1/stag-findsubtree.pl.1
>> Manifying blib/man1/stag-join.pl.1
>> Manifying blib/man1/stag-autoschema.pl.1
>> Manifying blib/man1/stag-db.pl.1
>> Manifying blib/man1/stag-flatten.pl.1
>> Manifying blib/man1/stag-splitter.pl.1
>> Manifying blib/man1/stag-diff.pl.1
>> Manifying blib/man1/stag-filter.pl.1
>> Manifying blib/man3/Data::Stag::StagDB.3pm
>> Manifying blib/man3/Data::Stag::SxprWriter.3pm
>> Manifying blib/man3/Data::Stag.3pm
>> Manifying blib/man3/Data::Stag::ChainHandler.3pm
>> Manifying blib/man3/Data::Stag::IndentParser.3pm
>> Manifying blib/man3/Data::Stag::Simple.3pm
>> Manifying blib/man3/Data::Stag::SAX2Stag.3pm
>> Manifying blib/man3/Data::Stag::Arr2HTML.3pm
>> Manifying blib/man3/Data::Stag::XSLHandler.3pm
>> Manifying blib/man3/Data::Stag::PerlWriter.3pm
>> Manifying blib/man3/Data::Stag::XSLTHandler.3pm
>> Manifying blib/man3/Data::Stag::DTDWriter.3pm
>> Manifying blib/man3/Data::Stag::Writer.3pm
>> Manifying blib/man3/Data::Stag::XMLWriter.3pm
>> Manifying blib/man3/Data::Stag::GraphHandler.3pm
>> Manifying blib/man3/Data::Stag::XMLParser.3pm
>> Manifying blib/man3/Data::Stag::StagImpl.3pm
>> Manifying blib/man3/Data::Stag::PodParser.3pm
>> Manifying blib/man3/Data::Stag::BaseGenerator.3pm
>> Manifying blib/man3/Data::Stag::IndentWriter.3pm
>> Manifying blib/man3/Data::Stag::HashDB.3pm
>> Manifying blib/man3/Data::Stag::null.3pm
>> Manifying blib/man3/Data::Stag::ITextParser.3pm
>> Manifying blib/man3/Data::Stag::BaseHandler.3pm
>> Manifying blib/man3/Data::Stag::ITextWriter.3pm
>> Manifying blib/man3/Data::Stag::SxprParser.3pm
>> CMUNGALL/Data-Stag-0.11.tar.gz
>> make -- OK
>> Warning (usually harmless): 'YAML' not installed, will not store persistent state
>> Running make test
>> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
>> t/autoschema.........ok
>> t/chainhandler.......ok
>> t/db.................ok
>> t/emptytag...........ok
>> 3/3 skipped: various reasons
>> t/get................ok
>> t/handlers...........ok
>> t/handlers2..........ok
>> 1/9 skipped: various reasons
>> t/hashdb.............ok
>> t/homol..............ok
>> t/parsestr...........ok
>> 6/6 skipped: various reasons
>> t/qmatch.............ok
>> t/roundtrip-attrs....ok
>> 5/5 skipped: various reasons
>> t/set-attrs..........ok
>> 3/3 skipped: various reasons
>> t/set................ok
>> t/sxpr...............ok
>> t/unhash.............ok
>> t/unset..............ok
>> t/write..............ok
>> t/xml1...............ok
>> 7/7 skipped: various reasons
>> t/xml2...............ok
>> 4/4 skipped: various reasons
>> All tests successful, 29 subtests skipped.
>> Files=20, Tests=102, 1 wallclock secs ( 1.17 cusr + 0.23 csys = 1.40 CPU)
>> CMUNGALL/Data-Stag-0.11.tar.gz
>> make test -- OK
>> Warning (usually harmless): 'YAML' not installed, will not store persistent state
>> Running make install
>> Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install'
>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>> ERROR: Can't create '/usr/local/bin'
>> mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479
>>
>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>> at -e line 1
>> make: *** [pure_site_install] Error 13
>> CMUNGALL/Data-Stag-0.11.tar.gz
>> make install -- NOT OK
>> Warning (usually harmless): 'YAML' not installed, will not store persistent state
>>
>>
>> *** (back in Bioperl Build.PL) ***
>> Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n
>> - ERROR: You chose to install Data::Stag but it failed to install
>> * Optional prerequisite Ace is not installed
>> (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace)
>> * Optional prerequisite Spreadsheet::ParseExcel is not installed
>> (wanted for parsing Excel files, used by Bio::SeqIO::excel)
>> * Optional prerequisite Math::Random is not installed
>> (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory)
>> * Optional prerequisite Graph is not installed
>> (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork)
>> * Optional prerequisite SVG::Graph is not installed
>> (wanted for creating SVG images, used by Bio::TreeIO::svggraph)
>> * Optional prerequisite SOAP::Lite is not installed
>> (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap)
>> * Optional prerequisite Bio::ASN1::EntrezGene is not installed
>> (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!])
>> * Optional prerequisite GraphViz is not installed
>> (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz)
>> * Optional prerequisite Array::Compare is not installed
>> (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork)
>> * Optional prerequisite Convert::Binary::C is not installed
>> (wanted for strider functionality, used by Bio::SeqIO::strider)
>> * Optional prerequisite Algorithm::Munkres is not installed
>> (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork)
>> * Optional prerequisite XML::Twig is not installed
>> (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils)
>> * Optional prerequisite Set::Scalar is not installed
>> (wanted for proper operation, used by Bio::Tree::Compatible)
>> * Optional prerequisite XML::Parser::PerlSAX is not installed
>> (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp)
>> * Optional prerequisite XML::SAX::Writer is not installed
>> (wanted for writing xml, used by Bio::SeqIO::tigrxml)
>> * Optional prerequisite Clone is not installed
>> (wanted for cloning objects, used by Bio::Tools::Primer3)
>> * Optional prerequisite XML::DOM::XPath is not installed
>> (wanted for parsing interpro features, used by Bio::FeatureIO::interpro)
>> * Optional prerequisite PostScript::TextBlock is not installed
>> (wanted for EPS output, used by Bio::Tree::Draw::Cladogram)
>>
>> ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions
>> of the modules indicated above before proceeding with this installation
>>
>> Checking features:
>> BioDBGFF.................disabled
>> * MySQL, Pg nor Oracle DBI drivers are installed
>> BioDBSeqFeature_mysql....disabled
>> - DBD::mysql is not installed
>> Network..................enabled
>> BioDBSeqFeature_BDB......enabled
>>
>> Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a]
>> - will install all scripts
>>
>> Do you want to run tests that require connection to servers across the internet
>> (likely to cause some failures)? y/n [n] n
>> - will not run internet-requiring tests
>> Deleting Build
>> Removed previous script 'Build'
>>
>> Creating new 'Build' script for 'BioPerl' version '1.006000'
>> Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test
>> Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS
>> Deleting blib/script/bp_sreformat.PLS.bak
>> blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl
>> Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS
>> Deleting blib/script/seqconvert.PLS.bak
>> blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl
>> Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS
>> Deleting blib/script/parse_hmmsearch.PLS.bak
>> blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl
>> Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS
>> Deleting blib/script/bp_seqret.PLS.bak
>> blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl
>> Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS
>> Deleting blib/script/tree2pag.PLS.bak
>> blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl
>> Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS
>> Deleting blib/script/meta_gff.PLS.bak
>> blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl
>> Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS
>> Deleting blib/script/nexus2nh.PLS.bak
>> blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl
>> Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS
>> Deleting blib/script/filter_search.PLS.bak
>> blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl
>> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS
>> blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl
>> Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS
>> Deleting blib/script/generate_histogram.PLS.bak
>> blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl
>> Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS
>> Deleting blib/script/heterogeneity_test.PLS.bak
>> blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl
>> Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS
>> Deleting blib/script/flanks.PLS.bak
>> blib/script/flanks.PLS -> blib/script/bp_flanks.pl
>> Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS
>> Deleting blib/script/split_seq.PLS.bak
>> blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl
>> Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS
>> Deleting blib/script/load_gff.PLS.bak
>> blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl
>> Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS
>> Deleting blib/script/biogetseq.PLS.bak
>> blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl
>> Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS
>> Deleting blib/script/bp_fetch.PLS.bak
>> blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl
>> Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS
>> Deleting blib/script/mutate.PLS.bak
>> blib/script/mutate.PLS -> blib/script/bp_mutate.pl
>> Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS
>> Deleting blib/script/process_sgd.PLS.bak
>> blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl
>> Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS
>> Deleting blib/script/bp_index.PLS.bak
>> blib/script/bp_index.PLS -> blib/script/bp_index.pl
>> Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS
>> Deleting blib/script/dbsplit.PLS.bak
>> blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl
>> Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS
>> Deleting blib/script/oligo_count.PLS.bak
>> blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl
>> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS
>> Deleting blib/script/bp_seqfeature_load.PLS.bak
>> blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl
>> Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS
>> Deleting blib/script/process_gadfly.PLS.bak
>> blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl
>> Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS
>> Deleting blib/script/hmmer_to_table.PLS.bak
>> blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl
>> Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS
>> Deleting blib/script/fastam9_to_table.PLS.bak
>> blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl
>> Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS
>> Deleting blib/script/biofetch_genbank_proxy.PLS.bak
>> blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl
>> Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS
>> Deleting blib/script/seq_length.PLS.bak
>> blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl
>> Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS
>> Deleting blib/script/extract_feature_seq.PLS.bak
>> blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl
>> Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS
>> Deleting blib/script/genbank2gff.PLS.bak
>> blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl
>> Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS
>> Deleting blib/script/taxid4species.PLS.bak
>> blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl
>> Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS
>> Deleting blib/script/bulk_load_gff.PLS.bak
>> blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl
>> Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS
>> Deleting blib/script/search2gff.PLS.bak
>> blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl
>> Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS
>> Deleting blib/script/blast2tree.PLS.bak
>> blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl
>> Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS
>> Deleting blib/script/make_mrna_protein.PLS.bak
>> blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl
>> Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS
>> Deleting blib/script/unflatten_seq.PLS.bak
>> blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl
>> Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS
>> Deleting blib/script/search2tribe.PLS.bak
>> blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl
>> Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS
>> Deleting blib/script/bioflat_index.PLS.bak
>> blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl
>> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS
>> Deleting blib/script/bp_seqfeature_delete.PLS.bak
>> blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl
>> Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS
>> Deleting blib/script/query_entrez_taxa.PLS.bak
>> blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl
>> Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS
>> Deleting blib/script/pairwise_kaks.PLS.bak
>> blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl
>> Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS
>> Deleting blib/script/fast_load_gff.PLS.bak
>> blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl
>> Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS
>> Deleting blib/script/chaos_plot.PLS.bak
>> blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl
>> Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS
>> Deleting blib/script/taxonomy2tree.PLS.bak
>> blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl
>> Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS
>> Deleting blib/script/bp_mrtrans.PLS.bak
>> blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl
>> Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS
>> Deleting blib/script/search2alnblocks.PLS.bak
>> blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl
>> Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS
>> Deleting blib/script/download_query_genbank.PLS.bak
>> blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl
>> Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS
>> Deleting blib/script/bp_nrdb.PLS.bak
>> blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl
>> Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS
>> Deleting blib/script/mask_by_search.PLS.bak
>> blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl
>> Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS
>> Deleting blib/script/gccalc.PLS.bak
>> blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl
>> Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS
>> Deleting blib/script/composite_LD.PLS.bak
>> blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl
>> Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS
>> Deleting blib/script/classify_hits_kingdom.PLS.bak
>> blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl
>> Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS
>> Deleting blib/script/aacomp.PLS.bak
>> blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl
>> Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS
>> Deleting blib/script/process_wormbase.PLS.bak
>> blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl
>> Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS
>> Deleting blib/script/local_taxonomydb_query.PLS.bak
>> blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl
>> Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS
>> Deleting blib/script/biblio.PLS.bak
>> blib/script/biblio.PLS -> blib/script/bp_biblio.pl
>> Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS
>> Deleting blib/script/seqretsplit.PLS.bak
>> blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl
>> Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS
>> Deleting blib/script/remote_blast.PLS.bak
>> blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl
>> Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS
>> Deleting blib/script/genbank2gff3.PLS.bak
>> blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl
>> Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS
>> Deleting blib/script/search2table.PLS.bak
>> blib/script/search2table.PLS -> blib/script/bp_search2table.pl
>> Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS
>> Deleting blib/script/search2BSML.PLS.bak
>> blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl
>> Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS
>> Deleting blib/script/translate_seq.PLS.bak
>> blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl
>> t/Align/AlignStats...........................ok
>> t/Align/AlignUtil............................ok
>> t/Align/SimpleAlign..........................ok
>> t/Align/TreeBuild............................ok
>> t/Align/Utilities............................ok
>> t/AlignIO/AlignIO............................ok 1/28
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Annotation class 'Bio::Annotation::TagTree' failed to load:
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, <GEN24> line 86.
>> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, <GEN24> line 86.
>> Compilation failed in require at Bio/Root/Root.pm line 420, <GEN24> line 86.
>>
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
>> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422
>> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183
>> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216
>> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137
>> STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484
>> STACK: t/AlignIO/AlignIO.t:51
>> -----------------------------------------------------------
>>
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
>> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185
>> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216
>> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137
>> STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484
>> STACK: t/AlignIO/AlignIO.t:51
>> -----------------------------------------------------------
>> # Looks like you planned 28 tests but only ran 7.
>> # Looks like your test died just after 7.
>> t/AlignIO/AlignIO............................dubious
>> Test returned status 255 (wstat 65280, 0xff00)
>> DIED. FAILED tests 8-28
>> Failed 21/28 tests, 25.00% okay
>> t/AlignIO/arp................................ok 1/48
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Annotation class 'Bio::Annotation::TagTree' failed to load:
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, <GEN0> line 86.
>> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, <GEN0> line 86.
>> Compilation failed in require at Bio/Root/Root.pm line 420, <GEN0> line 86.
>>
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
>> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422
>> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183
>> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216
>> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137
>> STACK: t/AlignIO/arp.t:25
>> -----------------------------------------------------------
>>
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
>> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185
>> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216
>> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137
>> STACK: t/AlignIO/arp.t:25
>> -----------------------------------------------------------
>> # Looks like you planned 48 tests but only ran 2.
>> # Looks like your test died just after 2.
>> t/AlignIO/arp................................dubious
>> Test returned status 255 (wstat 65280, 0xff00)
>> DIED. FAILED tests 3-48
>> Failed 46/48 tests, 4.17% okay
>> t/AlignIO/bl2seq.............................ok
>> t/AlignIO/clustalw...........................ok
>> t/AlignIO/emboss.............................ok
>> t/AlignIO/fasta..............................ok
>> t/AlignIO/largemultifasta....................ok
>> t/AlignIO/maf................................ok
>> t/AlignIO/mase...............................ok
>> t/AlignIO/mega...............................ok
>> t/AlignIO/meme...............................ok
>> t/AlignIO/metafasta..........................ok
>> t/AlignIO/msf................................ok
>> t/AlignIO/nexus..............................ok
>> t/AlignIO/pfam...............................ok
>> t/AlignIO/phylip.............................ok
>> t/AlignIO/po.................................ok
>> t/AlignIO/prodom.............................ok
>> t/AlignIO/psi................................ok
>> t/AlignIO/selex..............................ok
>> t/AlignIO/stockholm..........................ok
>> t/AlignIO/xmfa...............................ok
>> t/Alphabet...................................ok
>> t/Annotation/Annotation......................ok 1/159
>> # Failed test 'use Bio::Annotation::TagTree;'
>> # at t/Annotation/Annotation.t line 20.
>> # Tried to use 'Bio::Annotation::TagTree'.
>> # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112.
>> # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20.
>> # Compilation failed in require at (eval 37) line 2.
>> # BEGIN failed--compilation aborted at (eval 37) line 2.
>> t/Annotation/Annotation......................NOK 9/159
>> # Failed test 'default itext'
>> # at t/Annotation/Annotation.t line 307.
>> # 'ARRAY(0x100c02a48)'
>> # doesn't match '(?-xism:Name: CALM1)'
>>
>> # Failed test 'itext'
>> # at t/Annotation/Annotation.t line 315.
>> # 'ARRAY(0x100c02a48)'
>> # doesn't match '(?-xism:Name: CALM1)'
>> Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316.
>> # Looks like you planned 159 tests but only ran 119.
>> # Looks like you failed 3 tests of 119 run.
>> # Looks like your test died just after 119.
>> t/Annotation/Annotation......................dubious
>> Test returned status 255 (wstat 65280, 0xff00)
>> DIED. FAILED tests 9, 117, 119-159
>> Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%)
>> t/Annotation/AnnotationAdaptor...............ok
>> t/Assembly/Assembly..........................ok 1/51
>> # Failed (TODO) test at t/Assembly/Assembly.t line 35.
>> t/Assembly/Assembly..........................ok
>> t/Assembly/ContigSpectrum....................ok
>> t/Biblio/Biblio..............................ok
>> 1/24 skipped: various reasons
>> t/Biblio/References..........................ok
>> t/Biblio/biofetch............................skipped
>> all skipped: Network tests have not been requested
>> t/Biblio/eutils..............................skipped
>> all skipped: The optional module XML::Twig (or dependencies thereof) was not installed
>> t/ClusterIO/ClusterIO........................ok
>> 8/12 skipped: various reasons
>> t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found
>> Exception
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112.
>> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112.
>> Compilation failed in require at Bio/SeqIO/swiss.pm line 197.
>> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197.
>> Compilation failed in require at Bio/Root/Root.pm line 420.
>>
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
>> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422
>> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551
>> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372
>> STACK: t/ClusterIO/SequenceFamily.t:16
>> -----------------------------------------------------------
>>
>> 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 t/ClusterIO/SequenceFamily.t line 19.
>> # Looks like you planned 19 tests but only ran 2.
>> # Looks like your test died just after 2.
>> t/ClusterIO/SequenceFamily...................dubious
>> Test returned status 255 (wstat 65280, 0xff00)
>> DIED. FAILED tests 3-19
>> Failed 17/19 tests, 10.53% okay
>> t/ClusterIO/unigene..........................ok
>> t/Coordinate/CoordinateGraph.................ok
>> t/Coordinate/CoordinateMapper................ok
>> t/Coordinate/GeneCoordinateMapper............ok
>> t/LiveSeq/Chain..............................ok
>> t/LiveSeq/LiveSeq............................ok
>> t/LiveSeq/Mutation...........................ok
>> t/LiveSeq/Mutator............................ok
>> t/LocalDB/BioDBGFF...........................ok
>> 11/279 skipped: various reasons
>> t/LocalDB/BlastIndex.........................ok
>> t/LocalDB/DBFasta............................ok
>> t/LocalDB/DBQual.............................ok
>> t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found
>> Exception
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112.
>> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112.
>> Compilation failed in require at Bio/SeqIO/swiss.pm line 197.
>> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197.
>> Compilation failed in require at Bio/Root/Root.pm line 420.
>>
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
>> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422
>> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551
>> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372
>> STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338
>> STACK: t/LocalDB/Flat.t:89
>> -----------------------------------------------------------
>>
>> 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 Bio/DB/Flat/BinarySearch.pm line 346.
>> # Looks like you planned 24 tests but only ran 14.
>> # Looks like your test died just after 14.
>> t/LocalDB/Flat...............................dubious
>> Test returned status 255 (wstat 65280, 0xff00)
>> DIED. FAILED tests 15-24
>> Failed 10/24 tests, 58.33% okay
>> t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found
>> Exception
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112.
>> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112.
>> Compilation failed in require at Bio/SeqIO/swiss.pm line 197.
>> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197.
>> Compilation failed in require at Bio/Root/Root.pm line 420.
>>
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
>> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422
>> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551
>> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372
>> STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163
>> STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127
>> STACK: t/LocalDB/Index.t:91
>> -----------------------------------------------------------
>>
>> 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 "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128.
>> # Looks like you planned 64 tests but only ran 31.
>> # Looks like your test died just after 31.
>> t/LocalDB/Index..............................dubious
>> Test returned status 255 (wstat 65280, 0xff00)
>> DIED. FAILED tests 32-64
>> Failed 33/64 tests, 48.44% okay
>> t/LocalDB/Registry...........................ok
>> 9/14 skipped: various reasons
>> t/LocalDB/SeqFeature.........................ok
>> t/LocalDB/transfac_pro.......................ok
>> t/Map/Cyto...................................ok
>> t/Map/Linkage................................ok
>> t/Map/Map....................................ok
>> 19/267 skipped: various reasons
>> t/Map/MapIO..................................ok
>> t/Map/MicrosatelliteMarker...................ok
>> t/Map/Physical...............................ok
>> t/Matrix/IO/masta............................ok
>> t/Matrix/IO/psm..............................ok
>> t/Matrix/InstanceSite........................ok
>> t/Matrix/Matrix..............................ok
>> t/Matrix/ProtMatrix..........................ok
>> t/Matrix/ProtPsm.............................ok
>> 10/14 skipped: various reasons
>> t/Matrix/SiteMatrix..........................ok
>> t/Ontology/GOterm............................skipped
>> all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
>> t/Ontology/GraphAdaptor......................skipped
>> all skipped: The optional module Graph (or dependencies thereof) was not installed
>> t/Ontology/IO/go.............................skipped
>> all skipped: The optional module Graph (or dependencies thereof) was not installed
>> t/Ontology/IO/interpro.......................skipped
>> all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
>> t/Ontology/IO/obo............................skipped
>> all skipped: The optional module Graph (or dependencies thereof) was not installed
>> t/Ontology/Ontology..........................skipped
>> all skipped: The optional module Graph (or dependencies thereof) was not installed
>> t/Ontology/OntologyEngine....................skipped
>> all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
>> t/Ontology/OntologyStore.....................skipped
>> all skipped: The optional module Graph (or dependencies thereof) was not installed
>> t/Ontology/Relationship......................skipped
>> all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
>> t/Ontology/RelationshipType..................skipped
>> all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
>> t/Ontology/Term..............................skipped
>> all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
>> t/Perl.......................................ok
>> 10/29 skipped: various reasons
>> t/Phenotype/Correlate........................ok
>> t/Phenotype/MeSH.............................ok
>> t/Phenotype/Measure..........................ok
>> t/Phenotype/MiniMIMentry.....................ok
>> t/Phenotype/OMIMentry........................ok
>> t/Phenotype/OMIMentryAllelicVariant..........ok
>> t/Phenotype/OMIMparser.......................ok
>> t/Phenotype/Phenotype........................ok
>> t/PodSyntax..................................ok
>> t/PopGen/Coalescent..........................ok
>> t/PopGen/HtSNP...............................ok
>> t/PopGen/MK..................................ok
>> 4/46 skipped: various reasons
>> t/PopGen/PopGen..............................ok
>> t/PopGen/PopGenSims..........................ok
>> t/PopGen/TagHaplotype........................ok
>> t/RemoteDB/BioFetch..........................skipped
>> all skipped: Network tests have not been requested
>> t/RemoteDB/CUTG..............................ok
>> 14/37 skipped: various reasons
>> t/RemoteDB/DB................................skipped
>> all skipped: Network tests have not been requested
>> t/RemoteDB/EMBL..............................skipped
>> all skipped: Network tests have not been requested
>> t/RemoteDB/EUtilities........................skipped
>> all skipped: Network tests have not been requested
>> t/RemoteDB/HIV/HIV...........................ok
>> 13/30 skipped: various reasons
>> t/RemoteDB/HIV/HIVAnnotProcessor.............ok
>> t/RemoteDB/HIV/HIVQuery......................ok
>> 10/41 skipped: various reasons
>> t/RemoteDB/HIV/HIVQueryHelper................ok
>> t/RemoteDB/RefSeq............................ok
>> 10/16 skipped: various reasons
>> t/RemoteDB/SeqHound..........................skipped
>> all skipped: Network tests have not been requested
>> t/RemoteDB/SeqRead_fail......................skipped
>> all skipped: Network tests have not been requested
>> t/RemoteDB/SeqVersion........................ok
>> 8/10 skipped: various reasons
>> t/RemoteDB/Taxonomy..........................skipped
>> all skipped: The optional module XML::Twig (or dependencies thereof) was not installed
>> t/Restriction/Analysis.......................ok
>> t/Restriction/Gel............................ok
>> t/Restriction/IO.............................ok 1/18
>> # Failed (TODO) test at t/Restriction/IO.t line 31.
>> t/Restriction/IO.............................ok
>> 3/18 skipped: various reasons
>> t/Root/Exception.............................ok
>> t/Root/RootI.................................ok
>> t/Root/RootIO................................ok
>> 2/31 skipped: various reasons
>> t/Root/Storable..............................ok
>> t/Root/Tempfile..............................ok
>> t/Root/Utilities.............................ok
>> t/SearchDist.................................skipped
>> all skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed
>> t/SearchIO/CigarString.......................ok
>> t/SearchIO/GbrowseGFF........................ok
>> t/SearchIO/SearchIO..........................ok
>> t/SearchIO/SimilarityPair....................ok
>> t/SearchIO/Writer/HTMLWriter.................ok
>> t/SearchIO/Writer/HitTableWriter.............ok
>> t/SearchIO/blast.............................ok 1/1093
>> # Failed (TODO) test at t/SearchIO/blast.t line 527.
>> # '0.852'
>> # >
>> # '0.9'
>>
>> # Failed (TODO) test at t/SearchIO/blast.t line 528.
>> # '1.599'
>> # <=
>> # '1'
>> t/SearchIO/blast.............................ok
>> t/SearchIO/blast_pull........................ok 1/289
>> # Failed (TODO) test at t/SearchIO/blast_pull.t line 260.
>> # got: '0.946'
>> # expected: '0.943'
>> t/SearchIO/blast_pull........................ok
>> t/SearchIO/blasttable........................ok
>> t/SearchIO/blastxml..........................ok 1/298
>> # Failed (TODO) test at t/SearchIO/blastxml.t line 258.
>> # got: undef
>> # expected: '31984247'
>>
>> # Failed (TODO) test at t/SearchIO/blastxml.t line 259.
>> # got: undef
>> # expected: '88780'
>>
>> # Failed (TODO) test at t/SearchIO/blastxml.t line 260.
>> # got: undef
>> # expected: '49'
>> t/SearchIO/blastxml..........................ok
>> t/SearchIO/cross_match.......................ok
>> t/SearchIO/erpin.............................ok
>> t/SearchIO/exonerate.........................ok
>> 4/45 skipped: various reasons
>> t/SearchIO/fasta.............................ok
>> t/SearchIO/hmmer.............................ok
>> t/SearchIO/hmmer_pull........................ok
>> t/SearchIO/infernal..........................ok
>> t/SearchIO/megablast.........................ok
>> t/SearchIO/psl...............................ok
>> t/SearchIO/rnamotif..........................ok
>> t/SearchIO/sim4..............................ok
>> t/SearchIO/waba..............................ok
>> t/SearchIO/wise..............................ok
>> t/Seq/DBLink.................................ok
>> t/Seq/EncodedSeq.............................ok
>> t/Seq/LargeLocatableSeq......................ok
>> t/Seq/LargePSeq..............................ok
>> t/Seq/LocatableSeq...........................ok 1/116
>> # Failed (TODO) test at t/Seq/LocatableSeq.t line 45.
>> # got: 'Bio::Location::Simple=HASH(0x100838ce8)'
>> # expected: undef
>>
>> # Failed (TODO) test at t/Seq/LocatableSeq.t line 284.
>> # got: '\-\.=~'
>> # expected: '-\?'
>>
>> # Failed (TODO) test at t/Seq/LocatableSeq.t line 286.
>> # '19'
>> # ne
>> # '19'
>> t/Seq/LocatableSeq...........................ok
>> t/Seq/MetaSeq................................ok
>> t/Seq/PrimaryQual............................ok
>> t/Seq/PrimarySeq.............................ok
>> t/Seq/PrimedSeq..............................ok
>> t/Seq/Quality................................ok
>> t/Seq/Seq....................................ok
>> t/Seq/WithQuality............................ok
>> t/SeqEvolution...............................ok
>> t/SeqFeature/FeatureIO.......................skipped
>> all skipped: The optional module Graph (or dependencies thereof) was not installed
>> t/SeqFeature/Location........................ok
>> t/SeqFeature/LocationFactory.................ok
>> t/SeqFeature/Primer..........................ok
>> t/SeqFeature/Range...........................ok
>> t/SeqFeature/RangeI..........................ok
>> t/SeqFeature/SeqAnalysisParser...............ok
>> t/SeqFeature/SeqFeatAnnotated................skipped
>> all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
>> t/SeqFeature/SeqFeatCollection...............ok
>> t/SeqFeature/SeqFeature......................ok
>> 7/214 skipped: various reasons
>> t/SeqFeature/SeqFeaturePrimer................ok
>> t/SeqFeature/Unflattener.....................ok
>> t/SeqFeature/Unflattener2....................ok
>> t/SeqIO......................................ok
>> t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found
>> Exception
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112.
>> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112.
>> Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140.
>> BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140.
>> Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145.
>> BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145.
>> Compilation failed in require at Bio/Root/Root.pm line 420.
>>
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
>> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422
>> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551
>> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372
>> STACK: t/SeqIO/Handler.t:20
>> -----------------------------------------------------------
>>
>> 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 "verbose" on an undefined value at t/SeqIO/Handler.t line 23.
>> # Looks like you planned 550 tests but only ran 1.
>> # Looks like your test died just after 1.
>> t/SeqIO/Handler..............................dubious
>> Test returned status 255 (wstat 65280, 0xff00)
>> DIED. FAILED tests 2-550
>> Failed 549/550 tests, 0.18% okay
>> t/SeqIO/MultiFile............................ok
>> t/SeqIO/Multiple_fasta.......................ok
>> t/SeqIO/SeqBuilder...........................ok
>> t/SeqIO/Splicedseq...........................ok
>> t/SeqIO/abi..................................skipped
>> all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
>> t/SeqIO/ace..................................ok
>> t/SeqIO/agave................................ok
>> t/SeqIO/alf..................................skipped
>> all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
>> t/SeqIO/asciitree............................ok
>> t/SeqIO/bsml.................................skipped
>> all skipped: The optional module XML::DOM (or dependencies thereof) was not installed
>> t/SeqIO/bsml_sax.............................skipped
>> all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed
>> t/SeqIO/chadoxml.............................ok
>> t/SeqIO/chaos................................
>> # Failed test 'use Bio::SeqIO::chaos;'
>> # at t/SeqIO/chaos.t line 15.
>> # Tried to use 'Bio::SeqIO::chaos'.
>> # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132.
>> # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15.
>> # Compilation failed in require at (eval 14) line 2.
>> # BEGIN failed--compilation aborted at (eval 14) line 2.
>> # Looks like you failed 1 test of 8.
>> t/SeqIO/chaos................................dubious
>> Test returned status 1 (wstat 256, 0x100)
>> DIED. FAILED test 1
>> Failed 1/8 tests, 87.50% okay
>> t/SeqIO/chaosxml.............................skipped
>> all skipped: The optional module Data::Stag (or dependencies thereof) was not installed
>> t/SeqIO/ctf..................................skipped
>> all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
>> t/SeqIO/embl.................................ok
>> t/SeqIO/entrezgene...........................skipped
>> all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
>> t/SeqIO/excel................................skipped
>> all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed
>> t/SeqIO/exp..................................skipped
>> all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
>> t/SeqIO/fasta................................ok
>> t/SeqIO/fastq................................ok
>> t/SeqIO/flybase_chadoxml.....................ok
>> t/SeqIO/game.................................skipped
>> all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
>> t/SeqIO/gcg..................................ok 1/17
>> # Failed (TODO) test 'primary_id'
>> # at t/SeqIO/gcg.t line 54.
>> # got: 'Bio::PrimarySeq=HASH(0x100830bd0)'
>> # expected: 'roa1_drome'
>> t/SeqIO/gcg..................................ok
>> t/SeqIO/genbank..............................ok
>> t/SeqIO/interpro.............................skipped
>> all skipped: The optional module XML::DOM::XPath (or dependencies thereof) was not installed
>> t/SeqIO/kegg.................................ok
>> t/SeqIO/largefasta...........................ok
>> t/SeqIO/lasergene............................ok
>> t/SeqIO/locuslink............................skipped
>> all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
>> t/SeqIO/metafasta............................ok
>> t/SeqIO/phd..................................ok
>> t/SeqIO/pir..................................ok
>> t/SeqIO/pln..................................skipped
>> all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
>> t/SeqIO/qual.................................ok
>> t/SeqIO/raw..................................ok
>> t/SeqIO/scf..................................ok 1/59
>> # Failed (TODO) test 'accuracies'
>> # at t/SeqIO/scf.t line 78.
>> # got: 'ARRAY(0x100ac5648)'
>> # expected: '482'
>> t/SeqIO/scf..................................ok
>> t/SeqIO/strider..............................skipped
>> all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed
>> t/SeqIO/swiss................................
>> # Failed test 'use Bio::SeqIO::swiss;'
>> # at t/SeqIO/swiss.t line 12.
>> # Tried to use 'Bio::SeqIO::swiss'.
>> # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112.
>> # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12.
>> # Compilation failed in require at Bio/SeqIO/swiss.pm line 197.
>> # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197.
>> # Compilation failed in require at (eval 14) line 2.
>> # BEGIN failed--compilation aborted at (eval 14) line 2.
>> Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17.
>> # Looks like you planned 240 tests but only ran 1.
>> # Looks like you failed 1 test of 1 run.
>> # Looks like your test died just after 1.
>> t/SeqIO/swiss................................dubious
>> Test returned status 255 (wstat 65280, 0xff00)
>> DIED. FAILED tests 1-240
>> Failed 240/240 tests, 0.00% okay
>> t/SeqIO/tab..................................ok
>> t/SeqIO/table................................ok
>> 112/450 skipped: various reasons
>> t/SeqIO/tigr.................................ok
>> t/SeqIO/tigrxml..............................skipped
>> all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed
>> t/SeqIO/tinyseq..............................skipped
>> all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
>> t/SeqIO/ztr..................................skipped
>> all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
>> t/SeqTools/CodonTable........................ok
>> t/SeqTools/ECnumber..........................ok
>> t/SeqTools/GuessSeqFormat....................ok 1/49Bio::SeqIO: swiss cannot be found
>> Exception
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112.
>> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112.
>> Compilation failed in require at Bio/SeqIO/swiss.pm line 197.
>> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197.
>> Compilation failed in require at Bio/Root/Root.pm line 420.
>>
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
>> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422
>> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551
>> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372
>> STACK: t/SeqTools/GuessSeqFormat.t:62
>> -----------------------------------------------------------
>>
>> 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/SeqTools/GuessSeqFormat....................NOK 25/49
>> # Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64.
>> # '
>> # at t/SeqTools/GuessSeqFormat.t line 71.
>> # got: '0'
>> # expected: '1'
>> # Looks like you planned 49 tests but ran 1 extra.
>> # Looks like you failed 1 test of 50 run.
>> t/SeqTools/GuessSeqFormat....................dubious
>> Test returned status 1 (wstat 256, 0x100)
>> DIED. FAILED tests 25, 50
>> Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%)
>> t/SeqTools/OddCodes..........................ok
>> t/SeqTools/SeqPattern........................ok
>> t/SeqTools/SeqStats..........................ok
>> t/SeqTools/SeqUtils..........................ok
>> t/SeqTools/SeqWords..........................ok
>> t/Species....................................ok
>> 5/21 skipped: various reasons
>> t/Structure/IO...............................ok
>> t/Structure/Structure........................ok
>> t/Symbol.....................................ok
>> t/TaxonTree..................................skipped
>> all skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated
>> t/Tools/Alignment/Consed.....................ok
>> t/Tools/Analysis/DNA/ESEfinder...............skipped
>> all skipped: Network tests have not been requested
>> t/Tools/Analysis/Protein/Domcut..............skipped
>> all skipped: Network tests have not been requested
>> t/Tools/Analysis/Protein/ELM.................skipped
>> all skipped: Network tests have not been requested
>> t/Tools/Analysis/Protein/GOR4................skipped
>> all skipped: Network tests have not been requested
>> t/Tools/Analysis/Protein/HNN.................skipped
>> all skipped: Network tests have not been requested
>> t/Tools/Analysis/Protein/Mitoprot............skipped
>> all skipped: Network tests have not been requested
>> t/Tools/Analysis/Protein/NetPhos.............skipped
>> all skipped: Network tests have not been requested
>> t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found
>> Exception
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112.
>> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112.
>> Compilation failed in require at Bio/SeqIO/swiss.pm line 197.
>> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197.
>> Compilation failed in require at Bio/Root/Root.pm line 420.
>>
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
>> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422
>> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551
>> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372
>> STACK: t/Tools/Analysis/Protein/Scansite.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 t/Tools/Analysis/Protein/Scansite.t line 27.
>> # Looks like you planned 14 tests but only ran 4.
>> # Looks like your test died just after 4.
>> t/Tools/Analysis/Protein/Scansite............dubious
>> Test returned status 255 (wstat 65280, 0xff00)
>> DIED. FAILED tests 5-14
>> Failed 10/14 tests, 28.57% okay
>> t/Tools/Analysis/Protein/Sopma...............ok
>> 12/16 skipped: various reasons
>> t/Tools/EMBOSS/Palindrome....................ok
>> t/Tools/EUtilities/EUtilParameters...........ok
>> t/Tools/EUtilities/egquery...................ok
>> t/Tools/EUtilities/einfo.....................ok
>> t/Tools/EUtilities/elink_acheck..............ok
>> t/Tools/EUtilities/elink_lcheck..............ok
>> t/Tools/EUtilities/elink_llinks..............ok
>> t/Tools/EUtilities/elink_ncheck..............ok
>> t/Tools/EUtilities/elink_neighbor............ok
>> t/Tools/EUtilities/elink_neighbor_history....ok
>> t/Tools/EUtilities/elink_scores..............ok
>> t/Tools/EUtilities/epost.....................ok
>> t/Tools/EUtilities/esearch...................ok
>> t/Tools/EUtilities/espell....................ok
>> t/Tools/EUtilities/esummary..................ok
>> t/Tools/Est2Genome...........................ok
>> t/Tools/FootPrinter..........................ok
>> t/Tools/GFF..................................ok
>> t/Tools/Geneid...............................ok
>> t/Tools/Genewise.............................ok
>> t/Tools/Genomewise...........................ok
>> t/Tools/Genpred..............................ok
>> t/Tools/Hmmer................................ok
>> t/Tools/IUPAC................................ok
>> t/Tools/Lucy.................................ok
>> t/Tools/Match................................ok
>> t/Tools/Phylo/Gerp...........................ok
>> t/Tools/Phylo/Molphy.........................ok
>> t/Tools/Phylo/PAML...........................ok
>> t/Tools/Phylo/Phylip/ProtDist................ok
>> t/Tools/Primer3..............................skipped
>> all skipped: The optional module Clone (or dependencies thereof) was not installed
>> t/Tools/Promoterwise.........................ok
>> t/Tools/Pseudowise...........................ok
>> t/Tools/QRNA.................................ok
>> t/Tools/RandDistFunctions....................ok
>> t/Tools/RepeatMasker.........................ok
>> t/Tools/Run/RemoteBlast......................skipped
>> all skipped: Network tests have not been requested
>> t/Tools/Run/StandAloneBlast..................ok
>> 12/45 skipped: various reasons
>> t/Tools/Run/WrapperBase......................ok
>> t/Tools/Seg..................................ok
>> t/Tools/SiRNA................................ok
>> t/Tools/Sigcleave............................ok
>> t/Tools/Signalp..............................ok
>> t/Tools/Signalp/ExtendedSignalp..............ok
>> t/Tools/Sim4.................................ok
>> t/Tools/Spidey/Spidey........................ok
>> t/Tools/TandemRepeatsFinder..................ok
>> t/Tools/TargetP..............................ok
>> t/Tools/Tmhmm................................ok
>> t/Tools/ePCR.................................ok
>> t/Tools/pICalculator.........................ok
>> t/Tools/rnamotif.............................skipped
>> all skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated
>> t/Tools/tRNAscanSE...........................ok
>> t/Tree/Compatible............................skipped
>> all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed
>> t/Tree/Node..................................ok
>> t/Tree/PhyloNetwork/Factory..................skipped
>> all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
>> t/Tree/PhyloNetwork/GraphViz.................skipped
>> all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
>> t/Tree/PhyloNetwork/MuVector.................ok
>> t/Tree/PhyloNetwork/PhyloNetwork.............skipped
>> all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
>> t/Tree/PhyloNetwork/RandomFactory............skipped
>> all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
>> t/Tree/PhyloNetwork/TreeFactory..............skipped
>> all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
>> t/Tree/RandomTreeFactory.....................ok
>> t/Tree/Tree..................................ok
>> t/Tree/TreeIO................................ok
>> 2/74 skipped: various reasons
>> t/Tree/TreeIO/lintree........................ok
>> t/Tree/TreeIO/newick.........................ok
>> t/Tree/TreeIO/nexus..........................ok
>> t/Tree/TreeIO/nhx............................ok
>> t/Tree/TreeIO/phyloxml.......................ok
>> t/Tree/TreeIO/svggraph.......................ok
>> 3/4 skipped: various reasons
>> t/Tree/TreeIO/tabtree........................ok
>> t/Tree/TreeStatistics........................ok
>> t/Variation/AAChange.........................ok
>> t/Variation/AAReverseMutate..................ok
>> t/Variation/Allele...........................ok
>> t/Variation/DNAMutation......................ok
>> t/Variation/RNAChange........................ok
>> t/Variation/SNP..............................ok
>> t/Variation/SeqDiff..........................ok
>> t/Variation/Variation_IO.....................ok
>> 15/26 skipped: various reasons
>> Failed Test Stat Wstat Total Fail List of Failed
>> -------------------------------------------------------------------------------
>> t/AlignIO/AlignIO.t 255 65280 28 42 8-28
>> t/AlignIO/arp.t 255 65280 48 92 3-48
>> t/Annotation/Annotation.t 255 65280 159 83 9 117 119-159
>> t/ClusterIO/SequenceFamily.t 255 65280 19 34 3-19
>> t/LocalDB/Flat.t 255 65280 24 20 15-24
>> t/LocalDB/Index.t 255 65280 64 66 32-64
>> t/SeqIO/Handler.t 255 65280 550 1098 2-550
>> t/SeqIO/chaos.t 1 256 8 1 1
>> t/SeqIO/swiss.t 255 65280 240 479 1-240
>> t/SeqTools/GuessSeqFormat.t 1 256 49 2 25 50
>> t/Tools/Analysis/Protein/Scansite.t 255 65280 14 20 5-14
>> 57 tests and 313 subtests skipped.
>> Failed 11/318 test scripts. 970/17228 subtests failed.
>> Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU)
>> Failed 11/318 test programs. 970/17228 subtests failed.
>> Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install
>> Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS
>> Deleting blib/script/bp_sreformat.PLS.bak
>> blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl
>> Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS
>> Deleting blib/script/seqconvert.PLS.bak
>> blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl
>> Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS
>> Deleting blib/script/parse_hmmsearch.PLS.bak
>> blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl
>> Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS
>> Deleting blib/script/bp_seqret.PLS.bak
>> blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl
>> Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS
>> Deleting blib/script/tree2pag.PLS.bak
>> blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl
>> Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS
>> Deleting blib/script/meta_gff.PLS.bak
>> blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl
>> Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS
>> Deleting blib/script/nexus2nh.PLS.bak
>> blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl
>> Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS
>> Deleting blib/script/filter_search.PLS.bak
>> blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl
>> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS
>> blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl
>> Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS
>> Deleting blib/script/generate_histogram.PLS.bak
>> blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl
>> Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS
>> Deleting blib/script/heterogeneity_test.PLS.bak
>> blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl
>> Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS
>> Deleting blib/script/flanks.PLS.bak
>> blib/script/flanks.PLS -> blib/script/bp_flanks.pl
>> Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS
>> Deleting blib/script/split_seq.PLS.bak
>> blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl
>> Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS
>> Deleting blib/script/load_gff.PLS.bak
>> blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl
>> Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS
>> Deleting blib/script/biogetseq.PLS.bak
>> blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl
>> Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS
>> Deleting blib/script/bp_fetch.PLS.bak
>> blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl
>> Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS
>> Deleting blib/script/mutate.PLS.bak
>> blib/script/mutate.PLS -> blib/script/bp_mutate.pl
>> Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS
>> Deleting blib/script/process_sgd.PLS.bak
>> blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl
>> Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS
>> Deleting blib/script/bp_index.PLS.bak
>> blib/script/bp_index.PLS -> blib/script/bp_index.pl
>> Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS
>> Deleting blib/script/dbsplit.PLS.bak
>> blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl
>> Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS
>> Deleting blib/script/oligo_count.PLS.bak
>> blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl
>> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS
>> Deleting blib/script/bp_seqfeature_load.PLS.bak
>> blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl
>> Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS
>> Deleting blib/script/process_gadfly.PLS.bak
>> blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl
>> Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS
>> Deleting blib/script/hmmer_to_table.PLS.bak
>> blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl
>> Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS
>> Deleting blib/script/fastam9_to_table.PLS.bak
>> blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl
>> Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS
>> Deleting blib/script/biofetch_genbank_proxy.PLS.bak
>> blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl
>> Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS
>> Deleting blib/script/seq_length.PLS.bak
>> blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl
>> Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS
>> Deleting blib/script/extract_feature_seq.PLS.bak
>> blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl
>> Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS
>> Deleting blib/script/genbank2gff.PLS.bak
>> blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl
>> Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS
>> Deleting blib/script/taxid4species.PLS.bak
>> blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl
>> Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS
>> Deleting blib/script/bulk_load_gff.PLS.bak
>> blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl
>> Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS
>> Deleting blib/script/search2gff.PLS.bak
>> blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl
>> Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS
>> Deleting blib/script/blast2tree.PLS.bak
>> blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl
>> Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS
>> Deleting blib/script/make_mrna_protein.PLS.bak
>> blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl
>> Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS
>> Deleting blib/script/unflatten_seq.PLS.bak
>> blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl
>> Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS
>> Deleting blib/script/search2tribe.PLS.bak
>> blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl
>> Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS
>> Deleting blib/script/bioflat_index.PLS.bak
>> blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl
>> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS
>> Deleting blib/script/bp_seqfeature_delete.PLS.bak
>> blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl
>> Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS
>> Deleting blib/script/query_entrez_taxa.PLS.bak
>> blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl
>> Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS
>> Deleting blib/script/pairwise_kaks.PLS.bak
>> blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl
>> Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS
>> Deleting blib/script/fast_load_gff.PLS.bak
>> blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl
>> Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS
>> Deleting blib/script/chaos_plot.PLS.bak
>> blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl
>> Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS
>> Deleting blib/script/taxonomy2tree.PLS.bak
>> blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl
>> Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS
>> Deleting blib/script/bp_mrtrans.PLS.bak
>> blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl
>> Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS
>> Deleting blib/script/search2alnblocks.PLS.bak
>> blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl
>> Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS
>> Deleting blib/script/download_query_genbank.PLS.bak
>> blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl
>> Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS
>> Deleting blib/script/bp_nrdb.PLS.bak
>> blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl
>> Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS
>> Deleting blib/script/mask_by_search.PLS.bak
>> blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl
>> Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS
>> Deleting blib/script/gccalc.PLS.bak
>> blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl
>> Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS
>> Deleting blib/script/composite_LD.PLS.bak
>> blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl
>> Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS
>> Deleting blib/script/classify_hits_kingdom.PLS.bak
>> blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl
>> Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS
>> Deleting blib/script/aacomp.PLS.bak
>> blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl
>> Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS
>> Deleting blib/script/process_wormbase.PLS.bak
>> blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl
>> Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS
>> Deleting blib/script/local_taxonomydb_query.PLS.bak
>> blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl
>> Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS
>> Deleting blib/script/biblio.PLS.bak
>> blib/script/biblio.PLS -> blib/script/bp_biblio.pl
>> Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS
>> Deleting blib/script/seqretsplit.PLS.bak
>> blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl
>> Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS
>> Deleting blib/script/remote_blast.PLS.bak
>> blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl
>> Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS
>> Deleting blib/script/genbank2gff3.PLS.bak
>> blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl
>> Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS
>> Deleting blib/script/search2table.PLS.bak
>> blib/script/search2table.PLS -> blib/script/bp_search2table.pl
>> Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS
>> Deleting blib/script/search2BSML.PLS.bak
>> blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl
>> Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS
>> Deleting blib/script/translate_seq.PLS.bak
>> blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl
>> Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1
>> Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1
>> Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1
>> Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1
>> Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1
>> Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1
>> Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1
>> Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1
>> Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1
>> Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1
>> Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1
>> Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1
>> Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1
>> Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1
>> Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1
>> Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1
>> Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1
>> Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1
>> Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1
>> Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1
>> Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1
>> Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1
>> Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1
>> Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1
>> Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1
>> Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1
>> Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1
>> Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1
>> Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1
>> Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1
>> Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1
>> Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1
>> Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1
>> Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1
>> Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1
>> Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1
>> Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1
>> Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1
>> Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1
>> Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1
>> Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1
>> Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1
>> Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1
>> Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1
>> Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1
>> Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1
>> Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1
>> Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1
>> Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1
>> Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1
>> Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1
>> Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1
>> Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1
>> Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1
>> Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1
>> Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1
>> Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1
>> Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1
>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>> ERROR: Can't create '/usr/local/bin'
>> mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479
>>
>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>> at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
More information about the Bioperl-l
mailing list