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

Chris Fields cjfields at uiuc.edu
Thu Aug 16 15:55:05 EDT 2007


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


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