Bug #49950 for bioperl: Win32 issue

Wed Sep 23 11:14:30 2009 kmx [...] cpan.org - Ticket created

Subject:

Win32 issue - Permission denied

Hi, we are currently finalising Win32/strawberry perl (Oct2009 release), that should support Bio::Perl as we have included Berkeley DB library for Win32. Unfortunately I have experienced the following error: ... 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 Can't rename 'blib\script\bp_seqfeature_gff3.PLS' to 'blib\script\bp_seqfeature_gff3.pl': Permission denied at C:\strawberry\cpan\build\BioPerl-1.6.0-hsCo9P/Bio/Root/Build.pm line 227. ... It seems to be a problem during moving files from *.PLS to *.pl (I guess Windows is not able to delete the original [*.PLS] file). I try to investigate this further, I have submitted this RT currently just for record. -- kmx

Sat Sep 26 00:14:18 2009 cjfields [...] uiuc.edu - Correspondence added

On Wed Sep 23 11:14:30 2009, KMX wrote: Show quoted text

> Hi, > > we are currently finalising Win32/strawberry perl (Oct2009 release), > that should support Bio::Perl as we have included Berkeley DB library > for Win32. > > Unfortunately I have experienced the following error: > > ... > 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 > Can't rename 'blib\script\bp_seqfeature_gff3.PLS' to > 'blib\script\bp_seqfeature_gff3.pl': Permission denied at > C:\strawberry\cpan\build\BioPerl-1.6.0-hsCo9P/Bio/Root/Build.pm line 227. > ... > > It seems to be a problem during moving files from *.PLS to *.pl (I guess > Windows is not able to delete the original [*.PLS] file). I try to > investigate this further, I have submitted this RT currently just for > record. > > -- > kmx

Any more movement on this? I am planning on a 1.6.1 release in the next few days, so let me know if there is anything I can do. chris

Sat Sep 26 00:14:19 2009 The RT System itself - Status changed from 'new' to 'open'

Sat Sep 26 14:44:44 2009 kmx [...] volny.cz - Correspondence added

Subject:	Re: [rt.cpan.org #49950] Win32 issue - Permission denied
Date:	Sat, 26 Sep 2009 20:44:10 +0200
To:	bug-bioperl [...] rt.cpan.org
From:	kmx <kmx [...] volny.cz>

Hi Chris, Show quoted text

> Any more movement on this? I am planning on a 1.6.1 release in the next few days, so let > me know if there is anything I can do. >

Well, I still do not have a solution for this problem. Here are some observations I have made: 1) Problem occurs only when installing via "cpan Bio::Perl". When installing by - untargz - perl Build.pl - build test everything seems to work fine 2) I think that it is due to the fact that installation via cpan runs in this order - perl Build.pl - build - build test however copying/renaming the script files into blib/script/ is done twice 1. during "build" + 2. during "build test" and during the second round an error occurs because the target file already exists and cannot be overwritten. 3) Inspecting the blib/script/ directory revealed that for some reason the file bp_seqfeature_gff3.pl has an attribute READ-ONLY and that is probably the reason why i cannot be overwritten. The mystery is why only this one file and not the others. Setting read-only flag on for example *.pm files copied into "blib" subdir is sort of a standard behaviour on Win32; unfortunately Bio::Perl is using for me slightly unusual build method so it is quite hard for me to handle this. I am not giving up, but .... -- kmx

Sat Sep 26 16:50:29 2009 kmx [...] volny.cz - Correspondence added

Subject:	Re: [rt.cpan.org #49950] Win32 issue - Permission denied
Date:	Sat, 26 Sep 2009 22:49:49 +0200
To:	bug-bioperl [...] rt.cpan.org
From:	kmx <kmx [...] volny.cz>

Hi again, I have prepared a simple patch to handle the permission issue - it is neither nice nor clever but works (see attached bio_patch.diff). I am also attaching the complete install log (Bio::Perl latest SVN) from Win32/strawberry perl (5.10.1 - Oct2009-beta2) - please have a look as there are some minor issues you might be interested in: 1) Many warnings during some tests - "Subroutine xxxx redefined at yyyy" (I have absolutely no idea what the hell this comes from) 2) Attempting to delete some open files in t/LocalDB/SeqFeature.t (Bio/DB/SeqFeature/Store/LoadHelper.pm: sub DESTROY) 3) Attempting to delete some open files in t/LocalDB/transfac_pro.t None of the 3 above mentioned issues is a blocker. -- kmx

Index: Bio/Root/Build.pm =================================================================== --- Bio/Root/Build.pm (revision 16179) +++ Bio/Root/Build.pm (working copy) @@ -209,6 +209,8 @@ $final =~ s/^/bp_/ unless $final =~ /^bp/; # add the "bp" prefix $final = File::Spec->catfile($script_dir, $final); $self->log_info("$result -> $final\n"); + unlink $final; + warn "[WARNING] Deleting '$final' failed!\n" if (-e $final); File::Copy::move($result, $final) or die "Can't rename '$result' to '$final': $!"; } }

Download bioperl_on_win32_log.txt.gz
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Mon Sep 28 21:34:58 2009 cjfields [...] uiuc.edu - Correspondence added

On Sat Sep 26 16:50:29 2009, kmx@volny.cz wrote: Show quoted text

> Hi again, > > I have prepared a simple patch to handle the permission issue - it is > neither nice nor clever but works (see attached bio_patch.diff). > > I am also attaching the complete install log (Bio::Perl latest SVN) from > Win32/strawberry perl (5.10.1 - Oct2009-beta2) - please have a look as > there are some minor issues you might be interested in: > > 1) Many warnings during some tests - "Subroutine xxxx redefined at yyyy" > (I have absolutely no idea what the hell this comes from) > > 2) Attempting to delete some open files in t/LocalDB/SeqFeature.t > (Bio/DB/SeqFeature/Store/LoadHelper.pm: sub DESTROY) > > 3) Attempting to delete some open files in t/LocalDB/transfac_pro.t > > None of the 3 above mentioned issues is a blocker. > > -- > kmx

Committed a modification of your fix for the permissions issue in 1.6.0_6. Not sure about the others, but we can look into it. Will leave this open for the time being.

Tue Sep 29 01:41:44 2009 kmx [...] volny.cz - Correspondence added

Subject:	Re: [rt.cpan.org #49950] Win32 issue - Permission denied
Date:	Tue, 29 Sep 2009 07:40:53 +0200
To:	bug-bioperl [...] rt.cpan.org
From:	kmx <kmx [...] volny.cz>

cpan -i CJFIELDS/BioPerl-1.6.0_6.tar.gz now installs fine on Win32/strawberry (Oct2009-beta2) - all test PASS. -- kmx

Wed Oct 21 23:52:47 2009 cjfields [...] uiuc.edu - Correspondence added

On Tue Sep 29 01:41:44 2009, kmx@volny.cz wrote: Show quoted text

> cpan -i CJFIELDS/BioPerl-1.6.0_6.tar.gz > > now installs fine on Win32/strawberry (Oct2009-beta2) - all test PASS. > > -- > kmx

Thanks! Closing ticket.

Wed Oct 21 23:52:48 2009 cjfields [...] uiuc.edu - Status changed from 'open' to 'resolved'

Bug #49950 for bioperl: Win32 issue - Permission denied