[Bioperl-l] Problem with Bio::SeqIO::staden::read on Mac OS X

Mike Muratet muratem at eng.uah.edu
Fri Aug 17 10:03:22 EDT 2007



On Thu, 16 Aug 2007, Chris Fields wrote:

> Date: Thu, 16 Aug 2007 14:55:05 -0500
> From: Chris Fields <cjfields at uiuc.edu>
> To: muratem at eng.uah.edu
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Problem with Bio::SeqIO::staden::read on Mac OS X
> 
>
> On Aug 16, 2007, at 2:10 PM, muratem at eng.uah.edu wrote:
>
>> Hello
>> 
>> This might not be the correct list for this particular problem, but
>> hopefully someone can help. I am trying to install ...staden::read on a
>> Mac OS X 10.4. I tried installing cpan but it wouldn't work so I went to
>> the manual methods. Perl is on the system and appears to be installed
>> correctly for a Mac. Bioperl 1.5.2 was installed via fink and appears to
>> be OK also. I'm trying to install the Bio::SeqIO::staden::read module. I
>> downloaded the bioperl-ext-1.5.1 tarball from bioperl.org, did the usual
>> perl Makefile.PL and make and get:
>> 
>> newyork:/usr/local/bioperl-ext-1.5.1 root# make
>> Makefile:1148: *** multiple target patterns.  Stop.
>> 
>> A snippet from the Makefile...
>> 
>>    1148 pm_to_blib: $(TO_INST_PM)
>>    1149         $(NOECHO) $(PERLRUN) -MExtUtils::Install -e
>> 'pm_to_blib({@ARGV}, '\''$(INST_LIB)/auto'\'', '\''$(PM_FILTER)'\'')'\
>>    1150           Bio/Ext/Align/libs/hscore.h
>> $(INST_LIB)/Bio/Ext/Align/libs/hscore.h \
>>    1151           Bio/Ext/Align/libs/probability.c
>> $(INST_LIB)/Bio/Ext/Align/libs/probability.c \
>>    1152           Bio/Ext/Align/libs/linesubs.h
>> $(INST_LIB)/Bio/Ext/Align/libs/linesubs.h \
>>    1153           Bio/Ext/Align/test.pl $(INST_LIB)/Bio/Ext/Align/test.pl 
>> \
>>    1154           Bio/Ext/Align/libs/wiseoverlay.h
>> $(INST_LIB)/Bio/Ext/Align/libs/wiseoverlay.h \
>>    1155           Bio/Ext/Align/libs/proteinsw.h
>> $(INST_LIB)/Bio/Ext/Align/libs/proteinsw.h \
>>    1156           Bio/Ext/Align/libs/wisebase.h
>> $(INST_LIB)/Bio/Ext/Align/libs/wisebase.h \
>>    1157           Bio/Ext/Align/libs/seqaligndisplay.h
>> $(INST_LIB)/Bio/Ext/Align/libs/seqaligndisplay.h \
>>    1158           Bio/Ext/Align/libs/dyna.h
>> $(INST_LIB)/Bio/Ext/Align/libs/dyna.h \
>> 
>> The README says you don't have to build the whole package, so I descended
>> to the staden directory and did a Make and didn't get any problems
>> reported. But when I did a make test I get:
>> 
>> newyork:/usr/local/bioperl-ext-1.5.1/Bio/SeqIO/staden root# make test
>> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
>> "test_harness(0, '../blib/lib', '../blib/arch')" test.pl
>> test....Had problems bootstrapping Inline module 
>> 'Bio::SeqIO::staden::read'
>> 
>> Can't load
>> '/usr/local/bioperl-ext-1.5.1/Bio/SeqIO/staden/../blib/arch/auto/ 
>> Bio/SeqIO/staden/read/read.bundle'
>> for module Bio::SeqIO::staden::read:
>> dlopen(/usr/local/bioperl-ext-1.5.1/Bio/SeqIO/staden/../blib/arch/ 
>> auto/Bio/SeqIO/staden/read/read.bundle,
>> 2): Symbol not found: _curl_easy_init
>>   Referenced from:
>> /usr/local/bioperl-ext-1.5.1/Bio/SeqIO/staden/../blib/arch/auto/Bio/ 
>> SeqIO/staden/read/read.bundle
>>   Expected in: dynamic lookup
>>  at /Library/Perl/5.8.6/Inline.pm line 500
>> 
>> 
>>  at test.pl line 0
>> INIT failed--call queue aborted, <DATA> line 1.
>> test....dubious
>>         Test returned status 255 (wstat 65280, 0xff00)
>> DIED. FAILED tests 1-94
>>         Failed 94/94 tests, 0.00% okay
>> Failed Test Stat Wstat Total Fail  Failed  List of Failed
>> ---------------------------------------------------------------------- 
>> ---------
>> test.pl      255 65280    94  188 200.00%  1-94
>> Failed 1/1 test scripts, 0.00% okay. 94/94 subtests failed, 0.00% okay.
>> make: *** [test_dynamic] Error 2
>> 
>> The missing symbol is apparently from libcurl. I have both libcurl.2.dylib
>> and libcurl.3.dylib with copies in multiple locations including /usr/lib,
>> /usr/local/lib and the usual Mac directories. I used the Mac otool to look
>> at the externals in read.bundle and it references libz.1.dylib and
>> libSystem.B.dylib. Could this be a case where there should have been a
>> link to libcurl and wasn't?
>> 
>> I've searched the list and see only the Inline versioning problem (which I
>> had and fixed). Has anybody seen this problem before or built the module
>> on a Mac? How did you do it? Is this a question for the Staden list on
>> sourceforge?
>> 
>> Thanks
>> 
>> Mike
>
> Haven't seen the problem you list.  I have installed it on Mac OS X (intel) 
> w/o problems so I know it works; at least all tests passed though I remember 
> Inline complaining for some reason.
>
> You should try using bioperl-ext from CVS (it is really 1.5.1 but with 
> updated docs and maybe a change or two).  The process is a little tricky but 
> is documented in the README in the package.  You'll need the old io_lib 
> (1.8.12 or earlier) from Staden if memory serves.
>
> chris
>

Thanks, I'll give that a try.

Mike


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