[Bioperl-l] Re: Bioperl 1.2.alpha testing under cygwin. Was RE: [Bioperl-l] 1.2- alpha-1 tar file built

[Ewan Birney]

On Mon, 23 Dec 2002, Nash, John wrote:

> Bear with me - I'm a novice at this. I tested bioperl-1.2-alpha under
> cygwin, and here are the results of my tests.
>
> System config:
> The latest cygwin release (stock standard), using perl 5.6.1, under Windows
> XP, running on a Pentium III-933 box with 768 Mb RAM, and the
> Bundle::BioPerl modules as described in my previous email (i.e. all but Ace
> and the mysql one).
>
> Tests:
> - tar zxvfed the file, and did "perl Makefile.PL" - it caused a BIG fork
> error with libpng12.dll.
> - hit the cygwin mailing list archives, and learnt how to "rebase" DLLs
> (details can be supplied upon request).
> - perl Makefile.PL works (At least it doesn't crash any more - see below).
> - make returns: make: *** [pm_to_blib] Error 255
>
> In comparing this to my linux tests and to the bioperl 1.0.2 distribution
> under cygwin, I figured out that pm_to_blib was not being made, and files
> were not being moved to blib/lib/*.pod nor to blib/lib/Bio/.  Ewan suggested
> a "line too long" problem in Makefile. I'll look and see.
>
> Meanwhile, I re-made it on my Linux box and moved the relevant files across
> - made sure they were not Linux-specific, used the proper Makefile from
> cygwin and did the tests.
>
> Most of them worked - here are the tests that didn't pass.  I may have not
> found and transferred all of the files across for all of the tests to work -
> which may have caused some of the errors.  Any assistance to flatten the
> learning curve will be appreciated - I have never debugged 'make' before -
> but I'm keen.
>
> cheers,
> John
>
> << relevant results from "make test > test.log 2>&1" follow:
>
> PERL_DL_NONLAZY=1 /usr/local/bin/perl -Iblib/arch -Iblib/lib
> -I/usr/lib/perl5/5.6.1/cygwin-multi -I/usr/lib/perl5/5.6.1 -e 'use
> Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
>
> t/Assembly..........DB_File not installed. This means the Assembly modules
> are not available.  Skipping tests.
> ok

This is fine.

>
> t/DB................ok, 1/78 skipped: unknown reason
>

This is also fine.

> t/Index.............Usage: Cwd::cwd() at t/Index.t line 25.
> dubious
> 	Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-12
> 	Failed 12/12 tests, 0.00% okay
>

This is interesting. I will look into this.

> t/SearchIO..........Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> < remaining previously-noted warnings deleted here - JN>
>


These are well noted - Jason or steve is I hope will squash them; if not
me.

> ------------- EXCEPTION  -------------
> MSG: Could not open >searchio.out for reading: Permission denied
> STACK Bio::Root::IO::_initialize_io Bio/Root/IO.pm:260
> STACK Bio::Root::IO::new Bio/Root/IO.pm:206
> STACK Bio::SearchIO::new Bio/SearchIO.pm:123
> STACK Bio::SearchIO::new Bio/SearchIO.pm:155
> STACK toplevel t/SearchIO.t:981
>
> --------------------------------------
> dubious
> 	Test returned status 13 (wstat 3328, 0xd00)
> DIED. FAILED tests 663-718
> 	Failed 56/718 tests, 92.20% okay
>

This is more worrying - Jason - ideas? I haven't seen this before. Is your
file system protections ok (did you run this as a user which could write
into the . directory)

> t/SeqFeatCollection.DB_File not installed. This means the SeqFeatCollection
> wont work
> ok
>
> t/SeqIO.............ok, 3/146 skipped: unknown reason
>
> t/flat..............DB_File not loaded. This means flat.t test cannot be
> executed. Skipping
> ok
>
> t/game..............Use of uninitialized value in pattern match (m//) at
> /usr/lib/perl5/site_perl/5.6.1/XML/Writer.pm line 307.
> Use of uninitialized value in print at
> /usr/lib/perl5/5.6.1/cygwin-multi/IO/Handle.pm line 394.
> ok
>
> Failed Test  Status Wstat Total Fail  Failed  List of Failed
> ----------------------------------------------------------------------------
> ----
> t/Index.t   	   2   512    12   12 100.00%  1-12
> t/SearchIO.t	  13  3328   718   56   7.80%  663-718
> 4 subtests skipped.
> Failed 2/132 test scripts, 98.48% okay. 68/5948 subtests failed, 98.86%
> okay.
> make: *** [test_dynamic] Error 2
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>