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

[Nash, John]

More testing under cygwin:

When I wrote last, "make" was crashing (and causing disk errors which need
chkdsk to fix) - Ewan suspected a "Line too long" error in the Makefile.

The reason Makefile is puking, *is* a "line too long" error with respect to
pm_to_blib.  Since I can't really play with the Makefile - just for the sake
of a minor arch, I tried to see how I could increase command-line length
parameters under cygwin.  There was some suggestion in the mailing lists
that it could be Windows, but "nmake test" works under straight Windows, so
"I dunno".  I'll try and investigate more after my Xmas/New Year shutdown
ends and I have more resources at work.


Meanwhile to tests:

- updated from cvs on both my cygwin and Linux systems
- ran "perl Makefile.PL" on both.  
- made and tested under Linux (everything works on Redhat 7.3, except the
XML::Writer warnings previously described with t/game - also seen with
cygwin), and moved the missing files to the /blib subdirectory under cygwin
- ran "make test"
- Index.t and SearchIO.t failed and here is the log, with some commentary:

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/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

(JN)***Result of "perl t/Index.t > Index.log 2>&1":

1..12
Usage: Cwd::cwd() at t/Index.t line 25.


t/SearchIO..........
------------- 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:986

--------------------------------------
dubious
	Test returned status 13 (wstat 3328, 0xd00)
DIED. FAILED tests 665-720
	Failed 56/720 tests, 92.22% okay

t/SeqIO.............ok, 3/146 skipped: unknown reason


(JN) *** Result of "perl t/SearchIO.t > searchio.log 2>&1":
1..720

(JN) Successful tests from 1-636 deleted...
ok 637 # Significance parsing broken for GCG-BLAST Hits -- see HSP
ok 638 # Raw score parsing broken for GCG-BLAST Hits -- see HSP

------------- 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:986

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

(JN) No more tests after 638 - it crashes here.  I have full write
permissions here, PLUS, I chmod'd the subdirectory tree to 777.  I even
tried touching "searchio.out" to see of it would help - to no avail.


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   720   56   7.78%  665-720
4 subtests skipped.
Failed 2/134 test scripts, 98.51% okay. 68/6020 subtests failed, 98.87%
okay.
make: *** [test_dynamic] Error 2


cheers,
John