[Bioperl-l] Initial tests of bioperl-1.0 on 64bit Itanium / HP-UX ia64 11.20: success

[Chris Dagdigian]

{ Background for bioperl-l members; some time ago HP donated a 64-bit dual CPU
Itanium "i2000" workstation to us so that we can ensure that bioperl works on
upcoming 64 bit releases of HU-UX on Intel's new Itanium CPUs. This was a really
nice thing for HP to do and was apparently the result of someone inside HP
claiming that bioperl support was a "must have" for HP-UX! HP is also
encouraging us to use this machine to qualify biojava, etc. and they also don't
mind if we load the system up with Linux-64 as well. Good news all around, kudos
to HP }


So far I have only downloaded and installed bioperl-1.0 without any of the other
dependencies or third party apps.

Initial results were great:

(1) Test #1 bioperl-1.0 with no external dependencies installed

Summary: Cool, only 11 out of 3049 tests failed!

perl -v output: 5.6.0 built for 9000/777-hpux
uname -a ouput: HP-UX obf-i64 B.11.20 U ia64 1879297411 unlimited-user license

Output from 'make test':
=========================
 218 subtests skipped (most due to not-installed dependencies)
 Failed 5/93 test scripts, 94.62% ok
 11/3049 subtests failed, 99.64% ok

The tests scripts that failed outright are:

t/DBFasta.t (Reason: AnyDBM_File doesnt define an EXISTS method at
Bio/DB/Fasta.pm line 789 - someone should look at this one...)

t/GDB.t (Reason: LWP modules not installed; all tests skipped)

t/Index.t (Reason: unknown, error messages not helpful; all tests fail. Final
test warns that one of Storable, DB_File or File::Temp is not installed)

t/consed.t: (Reason: all tests pass actually but there is a warning thrown at
the end saying that count_sequence_with_grep() fails because "grep does not run
on this operating system") This is odd because grep does seem to be installed
and working on this system
 
t/flat.t (Reason: DB_File.pm is not part of this perl5 installation)


All in all we are in good shape. I'll re-run the tests after installing some
dependencies and will also test out the codebase from bioperl-live



-Chris










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