Module installation- architecture problems

[rjbioinf]

Hello, Basically I have no idea how to solve this problem I encounter when trying to install a BioPerl module. Essentially the output is below:

> Bio-SamTools-1.33 user$ ./Build test
Set up build environment without MacOSX10.5 SDK (will build i386 binar
+ies)
Set up build environment without MacOSX10.5 SDK (will build i386 binar
+ies)
Set up build environment without MacOSX10.5 SDK (will build i386 binar
+ies)
t/01sam.t .. Set up build environment without MacOSX10.5 SDK (will bui
+ld i386 binaries)
Can't load '/Users/user/Programs/Bio-SamTools-1.33/t/../blib/arch/auto
+/Bio/DB/Sam/Sam.bundle' for module Bio::DB::Sam: dlopen(/Users/user/P
+rograms/Bio-SamTools-1.33/t/../blib/arch/auto/Bio/DB/Sam/Sam.bundle, 
+2): no suitable image found.  Did find:
    /Users/user/Programs/Bio-SamTools-1.33/t/../blib/arch/auto/Bio/DB/
+Sam/Sam.bundle: mach-o, but wrong architecture at /usr/local/ActivePe
+rl-5.14/lib/DynaLoader.pm line 195.
 at t/01sam.t line 26
Compilation failed in require at t/01sam.t line 26.
BEGIN failed--compilation aborted at t/01sam.t line 26.
t/01sam.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 112/112 subtests 

Test Summary Report
-------------------
t/01sam.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 112 tests but ran 0.
Files=1, Tests=0,  0 wallclock secs ( 0.01 usr  0.00 sys +  0.19 cusr 
+ 0.03 csys =  0.23 CPU)
Result: FAIL
Failed 1/1 test programs. 0/0 subtests failed.

Obviously the problem is something to do with different "architectures", but I have no idea how to fix this... Any help greatly appreciated.

[davido]

Is it possible that you upgraded to a different version of Perl, not binary compatible with your previous installation of sam?

Could it be that sam needed to be compiled using the same C compiler and same flags as were used in compiling your Perl?

Could it be that 'sam' was compiled with an earlier C compiler version (and consequently earlier C libraries) than your current version of Perl?

I don't know that any of those issues are at the root of your problem, but in work I've done on Inline::CPP, I've seen that each of these are sources of trouble that can result in similar points of failure.

[rjbioinf]

Thanks for the reply. Hopefully i have encountered a more illuminating error when I try to build the Bio-SamTools :

>Bio-SamTools-1.33 acd$ ./Build 
Set up build environment without MacOSX10.5 SDK (will build i386 binar
+ies)
Set up build environment without MacOSX10.5 SDK (will build i386 binar
+ies)
Set up build environment without MacOSX10.5 SDK (will build i386 binar
+ies)
Building Bio-SamTools
gcc -I../samtools-0.1.17/ -I/usr/local/ActivePerl-5.14/lib/CORE -DXS_V
+ERSION="1.33" -DVERSION="1.33" -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wfo
+rmat=0 -c -fno-common -DPERL_DARWIN -arch i386 -DUSE_SITECUSTOMIZE -D
+PERL_RELOCATABLE_INCPUSH -fno-merge-constants -fno-strict-aliasing -p
+ipe -fstack-protector -O3 -o lib/Bio/DB/Sam.o lib/Bio/DB/Sam.c
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/Sam/Sam.bs')
env LD_RUN_PATH=/usr/local/ActivePerl-5.14/lib/CORE cc -mmacosx-versio
+n-min=10.5 -bundle -undefined dynamic_lookup -Wl,-search_paths_first 
+-arch i386 -fstack-protector -o blib/arch/auto/Bio/DB/Sam/Sam.bundle 
+lib/Bio/DB/Sam.o -L../samtools-0.1.17/ -lbam -lz
ld: warning: ignoring file ../samtools-0.1.17//libbam.a, file was buil
+t for archive which is not the architecture being linked (i386)

Does this mean the libbam.a was not compiled using i386 or that it was and should not have been?

[Anonymous Monk]

Essentially the output is below:

What output comes before that? Did you compile samtools yourself?

[rjbioinf]

Yes, Samtools is already compiled and works fine. Forgive me if you know this already, but Samtools is a separate collection of scripts. The Bio::DB::Sam, which i am trying to install provides an API to these functions. the installation instructions are:

perl Build.PL

./Build

./Build test

(sudo) ./Build install

I then run:

>Bio-SamTools-1.33 user$ perl Build.PL
This module requires samtools 0.1.10 or higher (samtools.sourceforge.n
+et).
Please enter the location of the bam.h and compiled libbam.a files: /U
+sers/user/Programs/samtools-0.1.17          

Found /Users/user/Programs/samtools-0.1.17/bam.h and /Users/user/Progr
+ams/samtools-0.1.17/libbam.a.
Set up build environment without MacOSX10.5 SDK (will build i386 binar
+ies)
Set up build environment without MacOSX10.5 SDK (will build i386 binar
+ies)
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-SamTools' version '1.33'

then:

> Bio-SamTools-1.33 user$ ./Build
Set up build environment without MacOSX10.5 SDK (will build i386 binar
+ies)
Set up build environment without MacOSX10.5 SDK (will build i386 binar
+ies)
Set up build environment without MacOSX10.5 SDK (will build i386 binar
+ies)
Building Bio-SamTools

then i run ./Build test and get the output detailed in the original post. thanks,