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This queue is for tickets about the Bio-SamTools CPAN distribution.

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The Basics
Id: 81118
Status: new
Priority: 0/
Queue: Bio-SamTools

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Owner: Nobody in particular
Requestors: pcantalupo [...] gmail.com
Cc:
AdminCc:

Bug Information
Severity: Important
Broken in: 1.36
Fixed in: (no value)



Subject: Test failed for Bio::DB::Sam
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Hi, I'm trying to install Bio-SamTools-1.36 on a Mac Server OS X 10.6.8. I am able to successfully compile Bio-SamTools on cpan command line with 'make Bio::DB::Sam' but when I try testing with 'test Bio::DB::Sam' I get the following error: ...SNIP Running Build test make: Nothing to be done for `all'. Use of uninitialized value $Test::Harness::Switches in length at /Users/pgc92/.cpan/build/Module-Build-0.3800-ypa0zj/blib/lib/Module/Build/Base.pm line 2760. t/01sam.t .. Can't load '/Users/pgc92/.cpan/build/Bio-SamTools-1.36-JyYhZl/t/../blib/arch/auto/Bio/DB/Sam/Sam.bundle' for module Bio::DB::Sam: dlopen(/Users/pgc92/.cpan/build/Bio-SamTools-1.36-JyYhZl/t/../blib/arch/auto/Bio/DB/Sam/Sam.bundle, 2): Symbol not found: _bam_nt16_rev_table Referenced from: /Users/pgc92/.cpan/build/Bio-SamTools-1.36-JyYhZl/t/../blib/arch/auto/Bio/DB/Sam/Sam.bundle Expected in: flat namespace in /Users/pgc92/.cpan/build/Bio-SamTools-1.36-JyYhZl/t/../blib/arch/auto/Bio/DB/Sam/Sam.bundle at /System/Library/Perl/5.10.0/darwin-thread-multi-2level/DynaLoader.pm line 207. at t/01sam.t line 26 Compilation failed in require at t/01sam.t line 26. BEGIN failed--compilation aborted at t/01sam.t line 26. t/01sam.t .. Dubious, test returned 2 (wstat 512, 0x200) Failed 112/112 subtests ...SNIP I think this error is related to http://bio.perl.org/pipermail/bioperl-l/2011-June/035241.html. Thank you for your help, Paul
From: pcantalupo [...] gmail.com
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Hi, Sorry I forgot to report on a few things: (63437) supernova:~ $ perl -v This is perl, v5.10.0 built for darwin-thread-multi-2level (with 2 registered patches, see perl -V for more detail) (63438) supernova:~ $ uname -a Darwin supernova 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 Thank you, Paul On Mon Nov 12 09:46:12 2012, pcantalupo wrote: Show quoted text
> Hi, > > I'm trying to install Bio-SamTools-1.36 on a Mac Server OS X 10.6.8. I > am able to successfully compile Bio-SamTools on cpan command line with > 'make Bio::DB::Sam' but when I try testing with 'test Bio::DB::Sam' I > get the following error: > > > ...SNIP > Running Build test > make: Nothing to be done for `all'. > Use of uninitialized value $Test::Harness::Switches in length at > /Users/pgc92/.cpan/build/Module-Build-0.3800- > ypa0zj/blib/lib/Module/Build/Base.pm > line 2760. > t/01sam.t .. Can't load > '/Users/pgc92/.cpan/build/Bio-SamTools-1.36- > JyYhZl/t/../blib/arch/auto/Bio/DB/Sam/Sam.bundle' > for module Bio::DB::Sam: > dlopen(/Users/pgc92/.cpan/build/Bio-SamTools-1.36- > JyYhZl/t/../blib/arch/auto/Bio/DB/Sam/Sam.bundle, > 2): Symbol not found: _bam_nt16_rev_table > Referenced from: > /Users/pgc92/.cpan/build/Bio-SamTools-1.36- > JyYhZl/t/../blib/arch/auto/Bio/DB/Sam/Sam.bundle > Expected in: flat namespace > in > /Users/pgc92/.cpan/build/Bio-SamTools-1.36- > JyYhZl/t/../blib/arch/auto/Bio/DB/Sam/Sam.bundle > at /System/Library/Perl/5.10.0/darwin-thread-multi- > 2level/DynaLoader.pm > line 207. > at t/01sam.t line 26 > Compilation failed in require at t/01sam.t line 26. > BEGIN failed--compilation aborted at t/01sam.t line 26. > t/01sam.t .. Dubious, test returned 2 (wstat 512, 0x200) > Failed 112/112 subtests > ...SNIP > > > I think this error is related to > http://bio.perl.org/pipermail/bioperl-l/2011-June/035241.html. Thank > you > for your help, > > Paul


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