[Bioperl-l] make test fails solaris 8 on "test_dynamic"

[Jason Stajich]

On Thu, 14 Mar 2002 Sciencelife@aol.com wrote:

> perl Makefile.PL ok
> "make" ok
>
> have gcc enviroment & utils preceeding path of
> Sun C/C++ compilers.  Environment works well
> for perl module compilation from cpan.
>
> 2 questions:
>
> How must bioperl environment be set differently from
> standard gcc ver. 3.03 & binutils2.11.2 environment?
> This environ works well for cpan module compilation.
>

There are no compiled modules in bioperl except the optional additional
bioperl-ext pkg.  so gcc, binutils have no bearing.

> How can user/passwd be set or passed to "make test" to
> circumvent inside proxy which prompts to authenticate
> for URLs beyond firewall?  "make test" gives no allowance for the prompt & fails attempting
> to visit external sites.

It doesn't really matter that these tests work, unless you have some
reason you really want to run the tests, we do a thorough job checking the
release before it goes out and do run tests on a sun solaris box.  There
is no way of sending proxy/firewall user/pass to the tests at this time
without adding some code to the test suite.  Anyone is welcome to add this
in to the tests if they feel inspired and we'll be happy to apply the
patches into CVS.

>
> Thanks for assistance.
>
> ------- errors for make test ------------
>
> MSG: 500 (Internal Server Error) Can't connect to www.gdb.org:80 (Timeout)
>
> Client-Date: Thu, 14 Mar 2002 22:51:33 GMT
>
> Error getting for url http://www.gdb.org/gdb-bin/genera/genera/hgd/GenomicSegment?displayName=D1S234&!action=q
> uery!
>
> -------------------- WARNING ---------------------
> MSG: Did not get any data for url http://www.gdb.org/gdb-bin/genera/genera/hgd/GenomicSegment?displayName=D1S2
> 34&!action=query
> ---------------------------------------------------
> Warning: Couldn't connect to GDB website with Bio::DB::GDB.pm!
> Error: Do you have network access? Skipping all other tests at t/GDB.t line 56.
> FAILED test 2
>         Failed 1/11 tests, 90.91% okay (-9 skipped tests: 1 okay, 9.09%)
> t/GFF...............ok
> t/Genpred...........ok
> t/HSP...............ok
> t/HTML..............ok
> t/Index.............ok
> t/LiveSeq...........ok
> t/Location..........ok
> t/Mutation..........ok
> t/Mutator...........ok
> t/OddCodes..........ok
> t/PrimarySeq........ok
> t/RNAChange.........ok
> t/Range.............ok
> t/RangeI............ok
> t/RestrictionEnzyme.ok
> t/RootI.............ok
> t/Sbjct.............ok
> t/SearchDist........ok, 3/3 skipped: unknown reason
> t/Seq...............ok
> t/SeqAnal...........ok
> t/SeqAnalysisParser.ok
> t/SeqDiff...........ok
> t/SeqFeature........ok
> t/SeqIO.............ok
> t/SeqPattern........ok
> t/SeqStats..........ok
> t/SeqUtils..........ok
> t/Sigcleave.........ok
> t/Sim4..............ok
>
> t/SimilarityPair....ok
> t/SimpleAlign.......ok
> t/Species...........ok
> t/StandAloneBlast...Blast program not found or not executable.
>   Blast can be obtained from ftp://ncbi.nlm.nih.gov/blast
> blast program not found. Skipping tests 3 to 8
> ok, 6/8 skipped: unknown reason
> t/TCoffee...........tcoffee program not found. Skipping tests 5 to 14.
> ok, 10/14 skipped: unknown reason
> t/Tempfile..........ok
> t/Tools.............ok
> t/UnivAln...........ok
> t/Variation_IO......
> The XML-format conversion requires the CPAN modules XML::Node, XML::Writer, and IO::String to be installed on
> your system, which they probably aren't. Skipping these tests.
> ok, 15/25 skipped: unknown reason
> t/WWW...............ok
> t/exception.........ok
> t/game..............XML::Parser::PerlSAX not loaded. This means game test cannot be executed. Skipping
> ok, 9/9 skipped: unknown reason
> t/hmmer.............ok
> t/largefasta........ok
> t/largepseq.........ok
> t/multiple_fasta....ok
> Failed Test Status Wstat Total Fail  Failed  List of Failed
> --------------------------------------------
> t/GDB.t                       11    1   9.09%  2
> 104 subtests skipped.
>
> Failed 1/60 test scripts, 98.33% okay. 1/1016 subtests failed, 99.90% okay.
> *** Error code 29
> make: Fatal error: Command failed for target `test_dynamic'
> -------------------------------------------------
>
>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu