Installing Bio::DB::Sam on a Mac

[Scott Cain-4]

Hi All,

Does anybody know if it is possible to get Bio::DB::Sam installed on a
Mac?  Up until now, I've always installed it on Linux systems.  While
samtools-0.1.6 builds fine, I get some warnings when trying to build
Bio::DB::Sam and test failures as well (see below).  There is a
message about libbam.a being "not of required architecture" but that
is a little surprising, as it resulted from the successful make
command when building Samtools from source.  Any suggestions?

Thanks,
Scott

$ perl Build.pl
This module requires samtools 0.1.4 or higher (samtools.sourceforge.net).
Please enter the location of the bam.h and compiled libbam.a files:
/Network/Servers/courses.cshl.edu/Volumes/protein/LDAPusers/bblackman/Desktop/samtools-0.1.6

...

$ ./Build

...

cc -I/Network/Servers/courses.cshl.edu/Volumes/protein/LDAPusers/bblackman/Desktop/samtools-0.1.6
-I/System/Library/Perl/5.8.8/darwin-thread-multi-2level/CORE
-DXS_VERSION="1.06" -DVERSION="1.06" -D_IOLIB=2 -D_FILE_OFFSET_BITS=64
-Wformat=0 -c -arch ppc -arch i386 -g -pipe -fno-common -DPERL_DARWIN
-no-cpp-precomp -fno-strict-aliasing -Wdeclaration-after-statement
-I/usr/local/include -O3 -o lib/Bio/DB/Sam.o lib/Bio/DB/Sam.c
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam_tell’:
lib/Bio/DB/Sam.xs:358: warning: ISO C90 forbids mixed declarations and code
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam_tell’:
lib/Bio/DB/Sam.xs:358: warning: ISO C90 forbids mixed declarations and code
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment__qscore’:
lib/Bio/DB/Sam.xs:524: warning: pointer targets in passing argument 2
of ‘Perl_newSVpv’ differ in signedness
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment_aux_keys’:
lib/Bio/DB/Sam.xs:628: warning: pointer targets in passing argument 2
of ‘Perl_newSVpv’ differ in signedness
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment_data’:
lib/Bio/DB/Sam.xs:651: warning: pointer targets in assignment differ
in signedness
lib/Bio/DB/Sam.xs:654: warning: pointer targets in passing argument 2
of ‘Perl_newSVpv’ differ in signedness
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment__qscore’:
lib/Bio/DB/Sam.xs:524: warning: pointer targets in passing argument 2
of ‘Perl_newSVpv’ differ in signedness
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment_aux_keys’:
lib/Bio/DB/Sam.xs:628: warning: pointer targets in passing argument 2
of ‘Perl_newSVpv’ differ in signedness
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment_data’:
lib/Bio/DB/Sam.xs:651: warning: pointer targets in assignment differ
in signedness
lib/Bio/DB/Sam.xs:654: warning: pointer targets in passing argument 2
of ‘Perl_newSVpv’ differ in signedness
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/Sam/Sam.bs')
env LD_RUN_PATH=/System/Library/Perl/5.8.8/darwin-thread-multi-2level/CORE
cc -mmacosx-version-min=10.5.8 -arch ppc -arch i386 -bundle -undefined
dynamic_lookup -L/usr/local/lib -o
blib/arch/auto/Bio/DB/Sam/Sam.bundle lib/Bio/DB/Sam.o
-L/Network/Servers/courses.cshl.edu/Volumes/protein/LDAPusers/bblackman/Desktop/samtools-0.1.6
-lbam -lz
ld warning: in /Network/Servers/courses.cshl.edu/Volumes/protein/LDAPusers/bblackman/Desktop/samtools-0.1.6/libbam.a,
file is not of required architecture

...

$ ./Build test
t/01sam....ok 1/93[fai_load] build FASTA index.
# Failed test 30 in t/01sam.t at line 135
#  t/01sam.t line 135 is:     ok($bam);
Can't call method "header_write" on an undefined value at t/01sam.t line 136.
t/01sam....dubious
        Test returned status 35 (wstat 8960, 0x2300)
DIED. FAILED tests 30-93
        Failed 64/93 tests, 31.18% okay
Failed Test Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/01sam.t     35  8960    93  127 136.56%  30-93
Failed 1/1 test scripts, 0.00% okay. 64/93 subtests failed, 31.18% okay.


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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