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

Sciencelife@aol.com Sciencelife@aol.com
Thu, 14 Mar 2002 18:15:18 EST


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.

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.

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'
-------------------------------------------------