[Bioperl-guts-l] [BioPerl - Bug #3215] CPAN build of Bioperl 1.6.900 in Win7 x64, Strawberry Perl 5.12.2 x64

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Thu Jun 16 21:24:28 EDT 2011


Issue #3215 has been updated by Francisco J. Ossandon.

File Git2_tests_results.txt added
File Git2_tests_results_no_redefined_logs.txt added

Chris Fields wrote:
> I added a simple overriding method in Bio::Root::Build to remove the '@$^W = 1@' line when the OS is Windows (needs testing).  The lack of a MANIFEST is due to the need to generate these on-the-fly prior to a release, in case new files need to be added or old ones removed (otherwise there is a conflict); having a persistent copy around doesn't make sense in this case.  If you really need it you can use '@./Build manifest@' to generate one.
> 
> Let me know if this helps, it has been pushed to the master branch on github.

I've updated to the current Git version and run the tests again, but the results are almost identical. The "redefined" warnings are still there, so it seems that removing those warnings is a lost case.

Also something that puzzles me are the "cannot unlink file" like this: "cannot unlink file for C:\Users\FRANCI~1\AppData\Local\Temp\Ev46vGf_1b\dbfa\7.fa: Permission denied at C:/strawberry/perl/lib/File/Temp.pm line 902"... since the Command Terminal is running as Administrator, how can it not have the permissions to clean the tests files???

I'm attaching the tests output (with and without the "redefined" lines), please look at the other warnings and exceptions, like the "RootIO.t" and "blast.t" fails. The "chmod" tests work in windows OS and NTFS or should be ommited entirely??

OS = Windows 7 Professional x64
Strawberry Perl = v5.12.2 built for MSWin32-x64-multi-thread
Git latest commit = d4e5412c92d9639fbf24a62f70ac5318aac21725
----------------------------------------
Bug #3215: CPAN build of Bioperl 1.6.900 in Win7 x64, Strawberry Perl 5.12.2 x64
https://redmine.open-bio.org/issues/3215

Author: Francisco J. Ossandon
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


Hello,
I've just tried to install Bioperl 1.6.900 in my system but failed. It seems there are problems in "t/Assembly/core.t" and "t/Root/RootIO.t".

I'm attaching the CPAN Reporter log file, since for some unknown reason it fails to send the report by itself (using the CPAN Testers 2.0 route).

As usual on Windows, its also infested with "subroutine xxx redefined at" warnings that don't appear in other OS. Is there a way to get rid of them?


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