[Bioperl-l] make test on Mac OS X

[Todd Richmond]

On 1/11/02 2:39 PM, "David Block" <dblock@gnf.org> wrote:

> Hello all,
> 
> Thanks to Hilmar's generosity ;) I am working on a TiBook running OS X.
> So I can do make test on OS X 10.1.
> 
> Unfortunately, make test doesn't finish.  It gets to
> t/EMBOSS............ok 1/4
> 
> and this hangs indefinitely.
> 
> dblock% perl -e 'print $^O,"\n"'
> darwin
> 
> So it's not a Mac thing, it's an OS X thing.
> 

I wouldn't say that... I ran a CVS update this evening and tried a make test
on my OS X machine. There was a problem with EMBOSS, but not a fatal one.

t/EMBOSS............ok 1/4Can't exec "wossname": No such file or directory
at blib/lib/Bio/Factory/EMBOSS.pm line 233.

And since I don't have EMBOSS installed, I guess that's fair.

There were a few other problems:

**********************************
t/SearchIO..........ok 160/290-------------------- WARNING
---------------------
MSG: unrecognized FASTA Family report file!
---------------------------------------------------
Can't call method "database_name" on an undefined value at t/SearchIO.t line
277, <GEN11> line 1.
t/SearchIO..........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 161-290
        Failed 130/290 tests, 55.17% okay

This fails because OS X is case insensitive and there is both a
HUMBETGLOA.FASTA and HUMBETGLOA.fasta in the /t/data directory.
The second HUMBETGLOA.fasta clobbers the first, and causes the test to fail.
When I changed HUMBETGLOA.FASTA to HUMBETGLOA.fas and changed SearchIO.t to
look for this file instead, all tests passed.


*********************************

t/consed............ok 11/12-------------------- WARNING
---------------------
MSG: Bio::Tools::Alignment::Consed::count_sequences_with_grep: This sub uses
grep which is doesn't run on this operating system, AFAIK. Sorry   .darwin
---------------------------------------------------
t/consed............FAILED test 12
        Failed 1/12 tests, 91.67% okay

The culprit here is the following line in Consed.pm:

        # I tried to cause graceful exiting if not on *ix here
        # then i took platforms from Bioperl*/PLATFORMS here. Is that good?
        # print("\$^O is $^O\n");
    if (!($^O =~ /dec_osf|linux|unix|bsd|solaris/i)) {

What OS X (darwin) doesn't count? A simple change to:

    if (!($^O =~ /dec_osf|linux|unix|bsd|solaris|darwin/i)) {

fixes this

***********************************

After those changes:

All tests successful, 97 subtests skipped.
Files=91, Tests=2121, 458 wallclock secs (95.64 cusr +  9.88 csys = 105.52
CPU)


-- 
Todd Richmond, PhD
http://cellwall.stanford.edu/todd
email: todd@verdant.stanford.edu