[Bioperl-l] environment variables (et al.) for bioperl-run tests
cjfields at illinois.edu
Tue Jan 6 14:22:18 EST 2009
On Jan 6, 2009, at 11:44 AM, Amir Karger wrote:
>> Amir Karger wrote:
>>> We just installed Bioperl-run on a cluster with very limited
>>> variables. So a huge number of tests failed.
>> None of the tests should fail. It's a bug if they do, so please let
>> know the details. When an environment variable isn't set or a
>> not installed, the test should skip, not fail.
> Oops! I lied. I should have more clearly stated that most of the tests
> nicely skipped, and some even told me that a certain environment
> variable should be set. The only things that actually broke are:
> t/AnalysisFactory_soap....10/12 proxy: transport protocol not
> # Looks like you planned 12 tests but only ran 11.
> # Looks like your test died just after 11.
> t/AnalysisFactory_soap.... Dubious, test returned 255 (wstat 65280,
> Failed 1/12 subtests
> Also, I got an error from RepeatMasker and Vista, which should
> be more graceful when things aren't in the PATH:
> t/RepeatMasker............Use of uninitialized value in concatenation
> (.) or string at
> ker.pm line 175.
> RepeatMasker program not found as or not executable.
> RepeatMasker program not found. Skipping tests 1 to 10.
> t/Vista...................readline() on closed filehandle PIPE at
> t/Vista.t line 39.
> Use of uninitialized value in numeric lt (<) at t/Vista.t line 53.
> You need at least version 1.2 of JDK to run vista
> It looks like the bug Chris referred me to is a bug to fix the above
> errors, which is great. But if all the tests pass and I haven't
> tested any of my bio binaries, I'm going to be kind of bummed when I
> actually try to use them. I'm not sure how flexible the testing
> mechanism is: is there an easy way to give the user a one-line
> when they run the test that says "The following binaries weren't found
> or did not have relevant environment variables set, so their subtests
> were skipped: blastall, clustalw, primer3, ...". That would be
> Even better would be if it referenced a file to look at or a wiki page
> listing how to set up PATH and other environment variables for each
> Sorry for the mis-type.
I'll look into the test fails if I can reproduce them (they'll be
archived with the bug report), and add that last bit as an enhancement
request to bugzilla.
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