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

muratem at eng.uah.edu muratem at eng.uah.edu
Thu Aug 16 15:10:34 EDT 2007


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



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