[Bioperl-l] OS X bioperl, staden/read, install problems (fwd)
Jason Stajich
jason at cgt.duhs.duke.edu
Sat Oct 4 08:37:23 EDT 2003
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
---------- Forwarded message ----------
Date: Fri, 3 Oct 2003 17:12:08 -0500
From: Jim Nolan <jnolan at tulane.edu>
To: Jason Stajich <jason at cgt.duhs.duke.edu>
Subject: Re: [Bioperl-l] OS X bioperl, staden/read, install problems
I get 29 errors in 'make test' for bioperl 1.2.3, asking for staden:read.
Here is a truncated output from the tests. I removed all the "ok"s
and truncated this part of the error message for staden:read:
"If this is a CPAN/distributed module, you may need to reinstall it on your
rsystem.
To allow Inline to compile the module in a temporary cache, simply remove the
Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module."
I get this error when I try to run my old scripts now.
The rest of the test output is below:
t/AlignIO....................ok 67/67One or more DATA sections were
not processed by Inline.
t/Biblio_biofetch............ok 11/11One or more DATA sections were
not processed by Inline.
t/BioDBGFF...................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/BioDBGFF.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/BioDBGFF...................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-120
Failed 120/120 tests, 0.00% okay
t/BioFetch_DB................ok 27/27One or more DATA sections were
not processed by Inline.
t/DB.........................ok 78/78One or more DATA sections were
not processed by Inline.
1/78 skipped:
t/EMBL_DB....................ok 15/15One or more DATA sections were
not processed by Inline.
t/FootPrinter................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/FootPrinter.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/FootPrinter................dubious
Test returned status 255 (wstat 65280, 0xff00)
after all the subtests completed successfully
t/Genewise...................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/Genewise.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/Genewise...................dubious
Test returned status 255 (wstat 65280, 0xff00)
after all the subtests completed successfully
t/Genpred....................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/Genpred.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/Genpred....................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-35
Failed 35/35 tests, 0.00% okay
t/Index......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/Index.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/Index......................dubious
Test returned status 255 (wstat 65280, 0xff00)
after all the subtests completed successfully
t/LiveSeq....................ok 48/48One or more DATA sections were
not processed by Inline.
t/LocusLink..................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/LocusLink.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/LocusLink..................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-23
Failed 23/23 tests, 0.00% okay
t/Mutator....................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/Mutator.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/Mutator....................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-13
Failed 13/13 tests, 0.00% okay
t/Perl.......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/Perl.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/Perl.......................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-14
Failed 14/14 tests, 0.00% okay
t/RefSeq.....................ok 3/13sleeping for 3 seconds
One or more DATA sections were not processed by Inline.
t/RepeatMasker...............The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/RepeatMasker.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/RepeatMasker...............dubious
Test returned status 255 (wstat 65280, 0xff00)
after all the subtests completed successfully
t/RootI......................ok 10/10One or more DATA sections were
not processed by Inline.
t/SeqAnalysisParser..........The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/SeqAnalysisParser.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/SeqAnalysisParser..........dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-11
Failed 11/11 tests, 0.00% okay
t/SeqBuilder.................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/SeqBuilder.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/SeqBuilder.................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-101
Failed 101/101 tests, 0.00% okay
t/SeqFeatCollection..........The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/SeqFeatCollection.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/SeqFeatCollection..........dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-428
Failed 428/428 tests, 0.00% okay
t/SeqFeature.................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/SeqFeature.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/SeqFeature.................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-62
Failed 62/62 tests, 0.00% okay
t/SeqIO......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/SeqIO.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/SeqIO......................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-184
Failed 184/184 tests, 0.00% okay
t/SequenceFamily.............The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/SequenceFamily.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/SequenceFamily.............dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-17
Failed 17/17 tests, 0.00% okay
t/SimilarityPair.............The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/SimilarityPair.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/SimilarityPair.............dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-5
Failed 5/5 tests, 0.00% okay
t/StandAloneBlast............The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/StandAloneBlast.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/StandAloneBlast............dubious
Test returned status 255 (wstat 65280, 0xff00)
after all the subtests completed successfully
t/Swiss......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/Swiss.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/Swiss......................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-5
Failed 5/5 tests, 0.00% okay
t/Tools......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/Tools.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/Tools......................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-8
Failed 8/8 tests, 0.00% okay
t/Variation_IO...............The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/Variation_IO.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/Variation_IO...............dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-25
Failed 25/25 tests, 0.00% okay
t/XEMBL_DB...................ok 2/9One or more DATA sections were not
processed by Inline.
t/ePCR.......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/ePCR.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/ePCR.......................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-23
Failed 23/23 tests, 0.00% okay
t/flat.......................ok 11/11One or more DATA sections were
not processed by Inline.
t/game.......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/game.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/game.......................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-23
Failed 23/23 tests, 0.00% okay
t/largefasta.................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/largefasta.t line 0
INIT failed--call queue aborted, <DATA> line 1.
Use of uninitialized value in unlink at t/largefasta.t line 16, <DATA> line 1.
t/largefasta.................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-15
Failed 15/15 tests, 0.00% okay
t/multiple_fasta.............The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/multiple_fasta.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/multiple_fasta.............dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-8
Failed 8/8 tests, 0.00% okay
t/phd........................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/phd.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/phd........................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-5
Failed 5/5 tests, 0.00% okay
t/primaryqual................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/primaryqual.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/primaryqual................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-31
Failed 31/31 tests, 0.00% okay
t/qual.......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/qual.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/qual.......................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-12
Failed 12/12 tests, 0.00% okay
t/scf........................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/scf.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/scf........................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-15
Failed 15/15 tests, 0.00% okay
t/splicedseq.................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
'/Library/Perl'
at t/splicedseq.t line 0
INIT failed--call queue aborted, <DATA> line 1.
t/splicedseq.................dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-9
Failed 9/9 tests, 0.00% okay
Failed Test Stat Wstat Total Fail Failed List of Failed
-------------------------------------------------------------------------------
t/BioDBGFF.t 255 65280 120 240 200.00% 1-120
t/FootPrinter.t 255 65280 20 0 0.00% ??
t/Genewise.t 255 65280 32 0 0.00% ??
t/Genpred.t 255 65280 35 70 200.00% 1-35
t/Index.t 255 65280 32 0 0.00% ??
t/LocusLink.t 255 65280 23 46 200.00% 1-23
t/Mutator.t 255 65280 13 26 200.00% 1-13
t/Perl.t 255 65280 14 28 200.00% 1-14
t/RepeatMasker.t 255 65280 6 0 0.00% ??
t/SeqAnalysisParser.t 255 65280 11 22 200.00% 1-11
t/SeqBuilder.t 255 65280 101 202 200.00% 1-101
t/SeqFeatCollection.t 255 65280 428 856 200.00% 1-428
t/SeqFeature.t 255 65280 62 124 200.00% 1-62
t/SeqIO.t 255 65280 184 368 200.00% 1-184
t/SequenceFamily.t 255 65280 17 34 200.00% 1-17
t/SimilarityPair.t 255 65280 5 10 200.00% 1-5
t/StandAloneBlast.t 255 65280 10 0 0.00% ??
t/Swiss.t 255 65280 5 10 200.00% 1-5
t/Tools.t 255 65280 8 16 200.00% 1-8
t/Variation_IO.t 255 65280 25 50 200.00% 1-25
t/ePCR.t 255 65280 23 46 200.00% 1-23
t/game.t 255 65280 23 46 200.00% 1-23
t/largefasta.t 255 65280 15 30 200.00% 1-15
t/multiple_fasta.t 255 65280 8 16 200.00% 1-8
t/phd.t 255 65280 5 10 200.00% 1-5
t/primaryqual.t 255 65280 31 62 200.00% 1-31
t/qual.t 255 65280 12 24 200.00% 1-12
t/scf.t 255 65280 15 30 200.00% 1-15
t/splicedseq.t 255 65280 9 18 200.00% 1-9
1 subtest skipped.
Failed 29/137 test scripts, 78.83% okay. 1192/6319 subtests failed,
81.14% okay.
make: *** [test_dynamic] Error 35
I never tried to install bioperl-ext before, but with all of these
errors, I figured it was a new dependency. some of the usual
dependencies I installed with fink, which mostly works OK (I
sometimes have to put a use/sw/libs/perl... line in scripts)
I appreciate your efforts to keep down the dependencies. Everything
was smooth for the last year or so on OS X.
Thanks again,
Jim
PS I was in the Duke Genetics Program, too. I was in the same class
as Tai-ping Sun.
I enjoyed the dUPG web page
>And you've tried with bioperl 1.2.3?
>
>But I'm a little confused -
>
> a) you do not need bioperl-ext unless you want to use the specialized
> stuff in there (c-extensions to bioperl modules).
>
> b) What test is giving you the warnings about IO::Staden - I can
> find no reference to it in any of the tests. Very weird error
> t/FootPrinter.t has nothing to do with Staden.
>
>We have tried very hard (or at least I advocate it very strongly) not to
>have a lot of dependancies, I think we are using a bare minimum of them,
>IO::String being one of the most essential. Lincoln even wrote
>his own socket based HTTP access to begin to remove LWP as a dependancy.
>
>What people need to remember is when it warns you about extra modules when
>you run perl Makefile.PL you don't HAVE To install all of those things,
>only those which are dependancies for functionality you want.
>
>
>-jason
>On Fri, 3 Oct 2003, Jim Nolan wrote:
>
>> I have been unable to install bioperl versions later than 1.2.1 on
> > Mac OS X. The first error I get is during 'make test':
> > "The extension 'Bio::SeqIO::staden::read' is not properly
>installed in path:
> > '/Library/Perl'
>> If this is a CPAN/distributed module, you may need to reinstall it on your
>> system.
>> To allow Inline to compile the module in a temporary cache, simply
>>remove the
>> Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module.
>> at t/FootPrinter.t line 0"
>> and numerous other tests.
>>
>> So I attempted to install bioperl-ext, which meant instaling the
>> Staden io_lib, though I don't use Staden. This had the difficulty of
>> errors caused by the locations of os.h and config.h
>> (http://portal.open-bio.org/mailman/htdig/bioperl-l/2003-June/012472.html).
>> I proceeded with the bioperl-ext install, using the directions at
>> http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html#bioperlxs
>> (which worked great until recently) I did the -fPIC edit, I did the
>> ranlib, but on make test for bioper-ext, I get:
>> /usr/bin/perl -I/System/Library/Perl/darwin -I/System/Library/Perl
>> /System/Library/Perl/ExtUtils/xsubpp -typemap
>> /System/Library/Perl/ExtUtils/typemap read.xs > read.xsc && mv
>> read.xsc read.c
>> cc -c -I/Users/jnolan/Desktop/download/bioperl-ext/Bio/SeqIO/staden
>> -I/usr/local/include/io_lib -g -pipe -pipe -fno-common
>> -no-cpp-precomp -flat_namespace -DHAS_TELLDIR_PROTOTYPE
>> -fno-strict-aliasing -Os -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\"
> > -I/System/Library/Perl/darwin/CORE read.c
> > In file included from /usr/local/include/io_lib/os.h:4,
> > from /usr/local/include/io_lib/Read.h:43,
>> from read.xs:5:
>> /usr/local/include/io_lib/config.h:45:1: warning: "VERSION" redefined
>> read.c:1:1: warning: this is the location of the previous definition
>> In file included from /usr/local/include/io_lib/translate.h:20,
>> from /usr/local/include/io_lib/Read.h:227,
>> from read.xs:5:
>> /usr/local/include/io_lib/expFileIO.h:42: parse error before "Exp_entries"
>> /usr/local/include/io_lib/expFileIO.h:42: warning: data definition
>> has no type o"
>> and lots of similar warnings.
>>
>> So it seems like there is still a problem with these libraries,
>> though I copied them where the compiler seems to be looking for them.
>>
>> Can someone point me in the right direction?
>>
>>
>> It would be great if there was a way to get rid of the dependency on
>> installing bioperl-ext to get bioperl to work. Even if the solution
>> for my particular problem is simple, the need to install additional
>> layers of dependencies takes a lot of the fun out of it for us lame
>> biological types ;-)
>> .
>>
>> Thanks.
>> Jim
>>
>
>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu
--
---------------------------------------------------------
Jim Nolan email:JNolan at tulane.edu
Department of Biochemistry SL43
Tulane University Health Sciences Center
1430 Tulane Ave. Phone: (504)-584-2453
New Orleans, LA 70112-2699 FAX: (504)-584-2739
http://www.tulane.edu/~biochem/faculty/nolan.htm
http://phage.bioc.tulane.edu
The requirements said: Windows 2000 or better.
So I got a Macintosh.
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