[Bioperl-l] Failed Istallation

Wesley Arthur wesleyarthur at optusnet.com.au
Fri Jan 9 08:11:15 UTC 2009 


----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Thursday, January 08, 2009 3:53 AM
Subject: Re: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2


> No copy-and-paste errors there.  Nope, none at all.  ;P
>
> -c
>
> On Jan 6, 2009, at 5:23 PM, Chris Fields wrote:
>
>> All,
>>
>> All,
>>
>> I am like to announce the second release candidate for BioPerl 1.6  is 
>> available for testing.
>>
>> A quick note on versioning: due to issues with alpha numbered  versions 
>> on CPAN possibly overwriting a stable release, this release  candidate 
>> has a VERSION of 1.005009_002 (or 1.005009002).  This will  be switched 
>> to 1.006000 (no alpha) once the release is final.
>>
>> The RC is currently being uploaded to CPAN and should be available  in 
>> the next 24-48 hours under authorname CJFIELDS.  In the meantime,  the 
>> release candidates can be directly downloaded here:
>>
>> http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2
>> http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz
>> http://bioperl.org/DIST/BioPerl-1.5.9_2.zip
>>
>> Signature file:
>> http://bioperl.org/DIST/SIGNATURES.md5
>>
>> A preliminary ActiveState PPM is also available and is located in  the 
>> BioPerl Release Candidate repository; the directions for  installation 
>> are here:
>>
>> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
>>
>> Please feel free to report issues with testing, installation, etc.  on 
>> the mail list and on this page:
>>
>> http://www.bioperl.org/wiki/Release_1.6_Testing
>>
>> Again, just to note we will be releasing bioperl-run, bioperl-db, 
>> bioperl-network, and others separately once the final 1.6 release is 
>> complete.
>>
>> Since the last release:
>>
>> Fixed:
>>
>> 1) Some cruft from testing the last release is no longer present.
>> 2) Several warnings and test failures (via CPAN Testers) now fixed.
>>
>> Known Issues:
>>
>> 1) A very recent change in ENSembl data causes one of the Map.t  tests to 
>> fail; this has already been fixed and will be present in  the next 
>> (final?) release.
>> 2) Some odd warnings for Bio::Assembly tests are still present, but  they 
>> are harmless.  Nevertheless they will be addressed prior to the  next 
>> release.
>> 3) Warnings for Bio::Annotation tests can be fixed by an upgrade to  the 
>> latest Data::Stag (this is NOT a required upgrade).
>> 4) PPM issues; note this is not high on our priority list ATM but I  will 
>> try to address it for the next release).
>>
>> Enjoy!
>>
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Dear Chris,
                 Thank you for the latest release of RC 1.5.9_2 with the 
ActiveState PPM.  My attempt to download this has failed.  I am using 
Windowas Vista and Activeperl 5.8.8.824.  The status tab  diplayed the 
following;

Synchronizing Database ...

  Downloading ActiveState Package Repository packlist ... done

  Updating ActiveState Package Repository database ... done

  Downloading BioPerl-Regular Releases packlist ... not modified

  Downloading Kobes packlist ... not modified

  Downloading Bribes  packlist ... done

  Updating Bribes  database ... done

  Downloading tcool packlist ... done

  Updating tcool database ... done

  Downloading BioPerl-Release Candidates packlist ... done

  Updating BioPerl-Release Candidates database ... done

Synchronizing Database done

BioPerl marked for install

BioPerl depends on Bundle-BioPerl-Core

BioPerl depends on Math-Random

BioPerl depends on Bio-ASN1-EntrezGene

BioPerl depends on Data-Stag

BioPerl depends on Algorithm-Munkres

BioPerl depends on GraphViz

BioPerl depends on XML-Writer

BioPerl depends on Graph

BioPerl depends on XML-DOM-XPath

BioPerl depends on PostScript

BioPerl depends on Spreadsheet-ParseExcel

BioPerl depends on XML-SAX

BioPerl depends on AcePerl

BioPerl depends on Array-Compare

BioPerl depends on Convert-Binary-C

BioPerl depends on XML-Twig

BioPerl depends on Set-Scalar

BioPerl depends on libxml-perl

BioPerl depends on XML-SAX-Writer

BioPerl depends on Clone

BioPerl depends on DB_File

BioPerl depends on IPC-Run

BioPerl depends on XML-DOM

BioPerl depends on XML-XPathEngine

BioPerl depends on IO-stringy

BioPerl depends on OLE-Storage_Lite

BioPerl depends on Ocsinventory-Agent

BioPerl depends on Cache-Cache

BioPerl depends on Text-Iconv

BioPerl depends on XML-Filter-BufferText

BioPerl depends on XML-NamespaceSupport

BioPerl depends on XML-RegExp

BioPerl depends on Error

Synchronizing Database ...

  Downloading ActiveState Package Repository packlist ... not modified

Synchronizing Database done

BioPerl marked for install

BioPerl depends on Bundle-BioPerl-Core

BioPerl depends on Math-Random

BioPerl depends on Bio-ASN1-EntrezGene

BioPerl depends on Data-Stag

BioPerl depends on Algorithm-Munkres

BioPerl depends on GraphViz

BioPerl depends on XML-Writer

BioPerl depends on Graph

BioPerl depends on XML-DOM-XPath

BioPerl depends on PostScript

BioPerl depends on Spreadsheet-ParseExcel

BioPerl depends on XML-SAX

BioPerl depends on AcePerl

BioPerl depends on Array-Compare

BioPerl depends on Convert-Binary-C

BioPerl depends on XML-Twig

BioPerl depends on Set-Scalar

BioPerl depends on libxml-perl

BioPerl depends on XML-SAX-Writer

BioPerl depends on Clone

BioPerl depends on DB_File

BioPerl depends on IPC-Run

BioPerl depends on XML-DOM

BioPerl depends on XML-XPathEngine

BioPerl depends on IO-stringy

BioPerl depends on OLE-Storage_Lite

BioPerl depends on Ocsinventory-Agent

BioPerl depends on Cache-Cache

BioPerl depends on Text-Iconv

BioPerl depends on XML-Filter-BufferText

BioPerl depends on XML-NamespaceSupport

BioPerl depends on XML-RegExp

BioPerl depends on Error

Installing 34 packages ...

  Downloading BioPerl-1.5.9_2 ... done

  Downloading Bundle-BioPerl-Core-1.5.9_2 ... done

  Downloading Math-Random-0.71 ... done

  Downloading Bio-ASN1-EntrezGene-1.09 ... done

  Downloading Data-Stag-0.11 ... done

  Downloading Algorithm-Munkres-0.08 ... done

  Downloading GraphViz-2.03 ... done

  Downloading XML-Writer-0.606 ... done

  Downloading Graph-0.90 ... done

  Downloading XML-DOM-XPath-0.14 ... done

  Downloading PostScript-0.06 ... done

  Downloading Spreadsheet-ParseExcel-0.43 ... done

  Downloading XML-SAX-0.96 ... done

  Downloading AcePerl-1.92 ... done

  Downloading Array-Compare-1.17 ... done

  Downloading Convert-Binary-C-0.71 ... done

  Downloading XML-Twig-3.32 ... done

  Downloading Set-Scalar-1.22 ... done

  Downloading libxml-perl-0.08 ... done

  Downloading XML-SAX-Writer-0.52 ... done

  Downloading Clone-0.29 ... done

  Downloading DB_File-1.816 ... done

  Downloading IPC-Run-0.82 ... done

  Downloading XML-DOM-1.44 ... done

  Downloading XML-XPathEngine-0.11 ... done

  Downloading IO-stringy-2.110 ... done

  Downloading OLE-Storage_Lite-0.18 ... done

  Downloading Ocsinventory-Agent-0.0.9.2 ... done

  Downloading Cache-Cache-1.05 ... done

  Downloading Text-Iconv-1.7 ... done

  Downloading XML-Filter-BufferText-1.01 ... done

  Downloading XML-NamespaceSupport-1.09 ... done

  Downloading XML-RegExp-0.03 ... done

  Downloading Error-0.17015 ... done

  Unpacking BioPerl-1.5.9_2 ... done

  Unpacking Bundle-BioPerl-Core-1.5.9_2 ... done

  Unpacking Math-Random-0.71 ... done

  Unpacking Bio-ASN1-EntrezGene-1.09 ... done

  Unpacking Data-Stag-0.11 ... done

  Unpacking Algorithm-Munkres-0.08 ... done

  Unpacking GraphViz-2.03 ... done

  Unpacking XML-Writer-0.606 ... done

  Unpacking Graph-0.90 ... done

  Unpacking XML-DOM-XPath-0.14 ... done

  Unpacking PostScript-0.06 ... done

  Unpacking Spreadsheet-ParseExcel-0.43 ... done

  Unpacking XML-SAX-0.96 ... done

  Unpacking AcePerl-1.92 ... done

  Unpacking Array-Compare-1.17 ... done

  Unpacking Convert-Binary-C-0.71 ... done

  Unpacking XML-Twig-3.32 ... done

  Unpacking Set-Scalar-1.22 ... done

  Unpacking libxml-perl-0.08 ... done

  Unpacking XML-SAX-Writer-0.52 ... done

  Unpacking Clone-0.29 ... done

  Unpacking DB_File-1.816 ... done

  Unpacking IPC-Run-0.82 ... done

  Unpacking XML-DOM-1.44 ... done

  Unpacking XML-XPathEngine-0.11 ... done

  Unpacking IO-stringy-2.110 ... done

  Unpacking OLE-Storage_Lite-0.18 ... done

  Unpacking Ocsinventory-Agent-0.0.9.2 ... done

  Unpacking Cache-Cache-1.05 ... done

  Unpacking Text-Iconv-1.7 ... done

  Unpacking XML-Filter-BufferText-1.01 ... done

  Unpacking XML-NamespaceSupport-1.09 ... done

  Unpacking XML-RegExp-0.03 ... done

  Unpacking Error-0.17015 ... done

  Generating HTML for BioPerl-1.5.9_2 ... done

  Generating HTML for Math-Random-0.71 ... done

  Generating HTML for Bio-ASN1-EntrezGene-1.09 ... done

  Generating HTML for Data-Stag-0.11 ... done

  Generating HTML for Algorithm-Munkres-0.08 ... done

  Generating HTML for GraphViz-2.03 ... done

  Generating HTML for XML-Writer-0.606 ... done

  Generating HTML for Graph-0.90 ... done

  Generating HTML for XML-DOM-XPath-0.14 ... done

  Generating HTML for PostScript-0.06 ... done

  Generating HTML for Spreadsheet-ParseExcel-0.43 ... done

  Generating HTML for XML-SAX-0.96 ... done

  Generating HTML for AcePerl-1.92 ... done

  Generating HTML for Array-Compare-1.17 ... done

  Generating HTML for Convert-Binary-C-0.71 ... done

  Generating HTML for XML-Twig-3.32 ... done

  Generating HTML for Set-Scalar-1.22 ... done

  Generating HTML for libxml-perl-0.08 ... done

  Generating HTML for XML-SAX-Writer-0.52 ... done

  Generating HTML for Clone-0.29 ... done

  Generating HTML for DB_File-1.816 ... done

  Generating HTML for IPC-Run-0.82 ... done

  Generating HTML for XML-DOM-1.44 ... done

  Generating HTML for XML-XPathEngine-0.11 ... done

  Generating HTML for IO-stringy-2.110 ... done

  Generating HTML for OLE-Storage_Lite-0.18 ... done

  Generating HTML for Ocsinventory-Agent-0.0.9.2 ... done

  Generating HTML for Cache-Cache-1.05 ... done

  Generating HTML for Text-Iconv-1.7 ... done

  Generating HTML for XML-Filter-BufferText-1.01 ... done

  Generating HTML for XML-NamespaceSupport-1.09 ... done

  Generating HTML for XML-RegExp-0.03 ... done

  Generating HTML for Error-0.17015 ... done

  Updating files in site area ... failed

Installing 34 packages failed



ERROR: File conflict for 'C:/Perl/html/site/lib/Bio/Align/AlignI.html'.

    The package bioperl has already installed a file that package BioPerl

    wants to install.

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