Re: Module installation- architecture problems

in reply to Module installation- architecture problems

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.

Dave

Comment on Re: Module installation- architecture problems

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Re^2: Module installation- architecture problems by rjbioinf (Acolyte) on Jun 05, 2012 at 11:50 UTC
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) [download] Does this mean the libbam.a was not compiled using i386 or that it was and should not have been?	[reply] [d/l]

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Re^2: Module installation- architecture problems
by rjbioinf (Acolyte) on Jun 05, 2012 at 11:50 UTC

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)
[download]

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

[reply]
[d/l]

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