[Bioperl-l] Problem installing CJFIELDS/BioPerl-1.6.1.tar.gz
Chad Davis
chad.a.davis at gmail.com
Fri Feb 4 13:20:16 UTC 2011
I may be off track here, but I saw a reference to GraphViz (though no
specific error) above. This reminded me of many problems I've had with
the GraphViz module over the last several years, though I think it's
better today. I generally had to, in CPAN:
force install GraphViz
before installing BioPerl. Make sure you have graphviz installed, first:
fink install graphviz
(I don't think 'graphviz-dev' is required?)
But, of course, it would be better to find the actual source of the
problem and fix it. If you could do:
test GraphViz
and report the errors, in addition to any other Bioperl tests that
might be failing.
Chad
On Fri, Feb 4, 2011 at 04:03, Scott Cain <scott at scottcain.net> wrote:
> Hi Anjan,
>
> Can you tell us what tests failed?
>
> Scott
>
>
> On Thu, Feb 3, 2011 at 5:20 PM, ANJAN PURKAYASTHA
> <anjan.purkayastha at gmail.com> wrote:
>> Hello,
>> I am unable to install distribution CJFIELDS/BioPerl-1.6.1.tar.gz on my Mac
>> 10.6.6.
>> Here is the tail end of the installation report:
>> Result: FAIL
>> Failed 9/329 test programs. 8/19347 subtests failed.
>> CJFIELDS/BioPerl-1.6.1.tar.gz
>> ./Build test -- NOT OK
>> //hint// to see the cpan-testers results for installing this module, try:
>> reports CJFIELDS/BioPerl-1.6.1.tar.gz
>> Warning (usually harmless): 'YAML' not installed, will not store persistent
>> state
>> Running Build install
>> make test had returned bad status, won't install without force
>> Could not read '/Users/anjan/.cpan/build/GraphViz-2.04-NQf6M6/META.yml'.
>> Falling back to other methods to determine prerequisites
>> Failed during this command:
>> SHLOMIF/Error-0.17016.tar.gz : install NO
>> JSWARTZ/Cache-Cache-1.06.tar.gz : install NO
>> LDS/AcePerl-1.92.tar.gz : install NO
>> JMCNAMARA/OLE-Storage_Lite-0.19.tar.gz : install NO
>> JMCNAMARA/Spreadsheet-ParseExcel-0.58.tar.gz : install NO
>> GROMMEL/Math-Random-0.71.tar.gz : install NO
>> JHI/Graph-0.94.tar.gz : install NO
>> JARW/Math-Spline-0.01.tar.gz : install NO
>> SHLOMIF/Statistics-Descriptive-3.0201.tar.gz : install NO
>> RONAN/SVG-2.50.tar.gz : install NO
>> JARW/Math-Derivative-0.01.tar.gz : install NO
>> COGENT/Tree-DAG_Node-1.06.tar.gz : install NO
>> ALLENDAY/SVG-Graph-0.02.tar.gz : install NO
>> ADAMK/Task-Weaken-1.03.tar.gz : install NO
>> ADAMK/Class-Inspector-1.25.tar.gz : install NO
>> MKUTTER/SOAP-Lite-0.712.tar.gz : install NO
>> CMUNGALL/Data-Stag-0.11.tar.gz : install NO
>> LBROCARD/GraphViz-2.04.tar.gz : writemakefile NO
>> '/usr/bin/perl Makefile.PL' returned status 512
>> TOKUHIROM/Test-Requires-0.06.tar.gz : install NO
>> DOY/Try-Tiny-0.09.tar.gz : install NO
>> RJBS/Test-Fatal-0.003.tar.gz : install NO
>> ADAMK/Params-Util-1.03.tar.gz : install NO
>> RJBS/Sub-Install-0.925.tar.gz : install NO
>> DROLSKY/Package-DeprecationManager-0.10.tar.gz: install NO
>> FLORA/MRO-Compat-0.11.tar.gz : install NO
>> DOY/Package-Stash-XS-0.21.tar.gz : install NO
>> DOY/Package-Stash-0.25.tar.gz : make_test NO
>> FLORA/Sub-Name-0.05.tar.gz : install NO
>> RJBS/Data-OptList-0.106.tar.gz : install NO
>> CHOCOLATE/Scope-Guard-0.20.tar.gz : install NO
>> RJBS/Sub-Exporter-0.982.tar.gz : install NO
>> FLORA/Devel-GlobalDestruction-0.03.tar.gz : install NO
>> FLORA/Class-MOP-1.12.tar.gz : make_test NO
>> DROLSKY/Moose-1.21.tar.gz : make_test NO
>> DAVECROSS/Array-Compare-2.01.tar.gz : make_test NO
>> MHX/Convert-Binary-C-0.74.tar.gz : install NO
>> TPEDERSE/Algorithm-Munkres-0.08.tar.gz : install NO
>> MIROD/XML-Twig-3.37.tar.gz : install NO
>> JHI/Set-Scalar-1.25.tar.gz : install NO
>> DCONWAY/Parse-RecDescent-1.965001.tar.gz : install NO
>> JMCNAMARA/Spreadsheet-WriteExcel-2.37.tar.gz : install NO
>> KMACLEOD/libxml-perl-0.08.tar.gz : install NO
>> RBERJON/XML-Filter-BufferText-1.01.tar.gz : install NO
>> PERIGRIN/XML-SAX-Writer-0.53.tar.gz : install NO
>> RDF/Clone-0.31.tar.gz : install NO
>> MIROD/XML-XPathEngine-0.12.tar.gz : install NO
>> TJMATHER/XML-RegExp-0.03.tar.gz : install NO
>> TJMATHER/XML-DOM-1.44.tar.gz : install NO
>> MIROD/XML-DOM-XPath-0.14.tar.gz : install NO
>> SHAWNPW/PostScript-0.06.tar.gz : install NO
>> CJFIELDS/BioPerl-1.6.1.tar.gz : make_test NO
>>
>> Any feedback on what may be going wrong will be immensley helpful.
>> Thanks,
>> Anjan
>>
>> --
>> ===================================
>> Anjan Purkayastha, PhD
>> Senior Computational Biologist
>> TessArae LLC
>> 46090 Lake Center Plaza, Suite 304
>> Potomac Falls, VA 20165**
>> Mobile-703.740.6939
>> ===================================
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D. scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Ontario Institute for Cancer Research
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
More information about the Bioperl-l
mailing list