[Bioperl-l] Bioperl 1.5.2 RC5

[Conrad Halling]

I compiled and installed Perl 5.8.8 under Mac OS X 10.4.8 into a 
directory named /test/perl. Then I used the cpan utility to attempt to 
install BioPerl 1.5.2 RC5 without having installed any of its dependencies.

The installation failed because of the following test failures:

  t/SeqFeature
  t/SeqHound_DB
  t/SeqVersion

Here are the pertinent details:

 t/SeqFeature.................IO::String or LWP::UserAgent or 
HTTP::Request not installed - skipping DB tests...
 Can't locate URI/Escape.pm in @INC (@INC contains: t 
/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib 
/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/arch 
/test/perl/lib/5.8.8/darwin-2level /test/perl/lib/5.8.8 
/test/perl/lib/site_perl/5.8.8/darwin-2level 
/test/perl/lib/site_perl/5.8.8 /test/perl/lib/site_perl .) at 
/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/SeqFeature/Annotated.pm 
line 86.
 BEGIN failed--compilation aborted at 
/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/SeqFeature/Annotated.pm 
line 86.
 Compilation failed in require at t/SeqFeature.t line 52.
 BEGIN failed--compilation aborted at t/SeqFeature.t line 52.
 t/SeqFeature.................dubious                                         

         Test returned status 2 (wstat 512, 0x200)
         after all the subtests completed successfully


 t/SeqHound_DB................ok 1/14Can't locate LWP/UserAgent.pm in 
@INC (@INC contains: 
/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib 
/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/arch 
/test/perl/lib/5.8.8/darwin-2level /test/perl/lib/5.8.8 
/test/perl/lib/site_perl/5.8.8/darwin-2level 
/test/perl/lib/site_perl/5.8.8 /test/perl/lib/site_perl .) at 
/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/WebDBSeqI.pm 
line 78.
 BEGIN failed--compilation aborted at 
/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/WebDBSeqI.pm 
line 78.
 Compilation failed in require at (eval 19) line 3.
         ...propagated at /test/perl/lib/5.8.8/base.pm line 85.
 BEGIN failed--compilation aborted at 
/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/SeqHound.pm 
line 88.
 Compilation failed in require at t/SeqHound_DB.t line 41.
 BEGIN failed--compilation aborted at t/SeqHound_DB.t line 41.
 Use of uninitialized value in -f at t/SeqHound_DB.t line 34.
 t/SeqHound_DB................dubious                                         

         Test returned status 2 (wstat 512, 0x200)
         after all the subtests completed successfully


 t/SeqVersion.................NOK 
1                                          
 #   Failed test 'use Bio::DB::SeqVersion;'
 #   in t/SeqVersion.t at line 21.
 #     Tried to use 'Bio::DB::SeqVersion'.
 #     Error:  Base class package "LWP::UserAgent" is empty.
 #     (Perhaps you need to 'use' the module which defines that package 
first.)
 #  at 
/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/WebAgent.pm 
line 90
 # BEGIN failed--compilation aborted at t/SeqVersion.t line 21.
 # Compilation failed in require at (eval 4) line 3.
 #       ...propagated at /test/perl/lib/5.8.8/base.pm line 85.
 # BEGIN failed--compilation aborted at 
/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/blib/lib/Bio/DB/SeqVersion.pm 
line 71.
 # Compilation failed in require at (eval 3) line 2.
 # BEGIN failed--compilation aborted at (eval 3) line 2.
 Can't locate object method "new" via package "Bio::DB::SeqVersion" at 
t/SeqVersion.t line 23.
 # Looks like you planned 10 tests but only ran 1.
 # Looks like you failed 1 test of 1 run.
 # Looks like your test died just after 1.
 t/SeqVersion.................dubious                                         

         Test returned status 255 (wstat 65280, 0xff00)
 DIED. FAILED tests 1-10
         Failed 10/10 tests, 0.00% okay


Failed Test     Stat Wstat Total Fail  Failed  List of Failed
 -------------------------------------------------------------------------------
 t/SeqFeature.t     2   512   211    0   0.00%  ??
 t/SeqHound_DB.t    2   512    14    0   0.00%  ??
 t/SeqVersion.t   255 65280    10   19 190.00%  1-10
 9 tests and 228 subtests skipped.
 Failed 3/235 test scripts, 98.72% okay. 10/11535 subtests failed, 
99.91% okay.
 make: *** [test_dynamic] Error 255
   /usr/bin/make test -- NOT OK
 Running make install
   make test had returned bad status, won't install without force


Sendu Bala wrote:
> Bioperl 1.5.2 Release Candidate 5 is ready and available for testing.
> See http://www.bioperl.org/wiki/Release_1.5.2 for
> instructions on getting and testing this RC.
>
[*snip*]
> Thank you,
> Sendu.

-- 
Conrad Halling
chhalling at verizon.net