[Bioperl-l] installing bioperl

Adam Witney awitney at sgul.ac.uk
Fri Jul 30 11:26:12 EDT 2010


It looks like it is trying to install and failing because of lack of permissions. I would recommend you try the cpan route like this:

perl -MCPAN -e shell

then from the cpan prompt, set a few things up (only need to do this once):

cpan> o conf make_install_make_command 'sudo make'
cpan> o conf mbuild_install_build_command 'sudo ./Build'
cpan> o conf commit

cpan> install CJFIELDS/BioPerl-1.6.1.tar.gz

.... and keep an eye on it... it will ask for a password early on to allow it to install into the right directories.

Or you if you want to retry your current method you could do this

sudo perl ./Build.pl

HTH

adam


On 30 Jul 2010, at 10:37, Carrie O'Malley 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
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> 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
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> 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
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> Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS
> Deleting blib/script/search2gff.PLS.bak
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> Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS
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> 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
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> Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS
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> Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS
> Deleting blib/script/bioflat_index.PLS.bak
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> 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
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> Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS
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> Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS
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> Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS
> Deleting blib/script/download_query_genbank.PLS.bak
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> 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
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> Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS
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> blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl
> Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS
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> Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS
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> Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS
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> Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS
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> Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS
> Deleting blib/script/local_taxonomydb_query.PLS.bak
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> Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS
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> blib/script/biblio.PLS -> blib/script/bp_biblio.pl
> Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS
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> 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
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> Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS
> Deleting blib/script/genbank2gff3.PLS.bak
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> Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS
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> Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS
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> 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




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