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

[Nash, John]

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

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

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

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>

------------- 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

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