[Bioperl-l] Bio::DB::Sam

Mon Feb 28 03:08:46 UTC 2011

Check the README; my guess is you need to compile samtools with the -fPIC flag:

http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.27/README

Could also be an out-of-date version of samtools itself, the latest Bio-Samtools requires v.0.1.9 or higher.

chris

On Feb 27, 2011, at 8:52 PM, Dan Kortschak wrote:

> Sorry for a post not strictly bioperl related, but I figured this forum
> will get the best appropriate coverage and Lincoln is often here.
> 
> I have just tried to install Bio::DB::Sam on a new server I have been
> tasked with setting up, but it fails to build with:
> 
> cpan[2]> install LDS/Bio-SamTools-1.27.tar.gz
> Running make for L/LD/LDS/Bio-SamTools-1.27.tar.gz
> 
>  CPAN: checksum security checks disabled because Digest::SHA not installed.
>  Please consider installing the Digest::SHA module.
> 
> Scanning cache /root/.cpan/build for sizes
> ............................................................................DONE
> CPAN: Archive::Tar loaded ok (v1.76)
> Bio-SamTools-1.27
> Bio-SamTools-1.27/Changes
> Bio-SamTools-1.27/LICENSE
> Bio-SamTools-1.27/DISCLAIMER
> Bio-SamTools-1.27/Build.PL
> Bio-SamTools-1.27/typemap
> Bio-SamTools-1.27/META.yml
> Bio-SamTools-1.27/README
> Bio-SamTools-1.27/MANIFEST
> Bio-SamTools-1.27/bin
> Bio-SamTools-1.27/bin/bamToGBrowse.pl
> Bio-SamTools-1.27/lib
> Bio-SamTools-1.27/lib/Bio
> Bio-SamTools-1.27/lib/Bio/DB
> Bio-SamTools-1.27/lib/Bio/DB/Sam.pm
> Bio-SamTools-1.27/lib/Bio/DB/Sam.xs
> Bio-SamTools-1.27/lib/Bio/DB/Sam
> Bio-SamTools-1.27/lib/Bio/DB/Sam/SamToGBrowse.pm
> Bio-SamTools-1.27/lib/Bio/DB/Sam/Constants.pm
> Bio-SamTools-1.27/lib/Bio/DB/Sam/Segment.pm
> Bio-SamTools-1.27/lib/Bio/DB/Bam
> Bio-SamTools-1.27/lib/Bio/DB/Bam/Alignment.pm
> Bio-SamTools-1.27/lib/Bio/DB/Bam/Target.pm
> Bio-SamTools-1.27/lib/Bio/DB/Bam/FetchIterator.pm
> Bio-SamTools-1.27/lib/Bio/DB/Bam/PileupWrapper.pm
> Bio-SamTools-1.27/lib/Bio/DB/Bam/AlignWrapper.pm
> Bio-SamTools-1.27/lib/Bio/DB/Bam/Query.pm
> Bio-SamTools-1.27/lib/Bio/DB/Bam/Pileup.pm
> Bio-SamTools-1.27/lib/Bio/DB/Bam/ReadIterator.pm
> Bio-SamTools-1.27/t
> Bio-SamTools-1.27/t/01sam.t
> Bio-SamTools-1.27/t/data
> Bio-SamTools-1.27/t/data/ex1.sam.gz
> Bio-SamTools-1.27/t/data/dm3_3R_4766911_4767130.sam.bam
> Bio-SamTools-1.27/t/data/ex1.bam
> Bio-SamTools-1.27/t/data/dm3_3R_4766911_4767130.sam
> Bio-SamTools-1.27/t/data/00README.txt
> Bio-SamTools-1.27/t/data/dm3_3R_4766911_4767130.sam.sorted.bam
> Bio-SamTools-1.27/t/data/ex1.fa
> CPAN: File::Temp loaded ok (v0.22)
> 
>  CPAN.pm: Going to build L/LD/LDS/Bio-SamTools-1.27.tar.gz
> 
> This module requires samtools 0.1.9 or higher (samtools.sourceforge.net).
>                                                                                                                                                                        Can't ioctl TIOCGETP: Invalid argument
> Consider installing Term::ReadKey from CPAN site nearby
> 	at http://www.perl.com/CPAN
> Or use
> 	perl -MCPAN -e shell
> to reach CPAN. Falling back to 'stty'.
> 	If you do not want to see this warning, set PERL_READLINE_NOWARN
> in your environment.
> Please enter the location of the bam.h and compiled libbam.a files: /usr/local/src/samtools_latest
> 
> Found /usr/local/src/samtools_latest/bam.h and /usr/local/src/samtools_latest/libbam.a.
> Creating new 'MYMETA.yml' with configuration results
> Creating new 'Build' script for 'Bio-SamTools' version '1.27'
> CPAN: Module::Build loaded ok (v0.3624)
> Building Bio-SamTools
> gcc -I/usr/local/src/samtools_latest -I/usr/lib64/perl5/CORE -DXS_VERSION="1.27" -DVERSION="1.27" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wformat=0 -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -o lib/Bio/DB/Sam.o lib/Bio/DB/Sam.c
> lib/Bio/DB/Sam.xs: In function ‘invoke_pileup_callback_fun’:
> lib/Bio/DB/Sam.xs:106: warning: unused variable ‘pileup_obj’
> lib/Bio/DB/Sam.c: In function ‘XS_Bio__DB__Bam_open’:
> lib/Bio/DB/Sam.c:530: warning: unused variable ‘packname’
> lib/Bio/DB/Sam.c: In function ‘XS_Bio__DB__Bam_index_build’:
> lib/Bio/DB/Sam.c:590: warning: unused variable ‘packname’
> lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam_sort_core’:
> lib/Bio/DB/Sam.xs:306: warning: implicit declaration of function ‘bam_sort_core’
> lib/Bio/DB/Sam.c:614: warning: unused variable ‘packname’
> lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam_tell’:
> lib/Bio/DB/Sam.xs:350: warning: format ‘%llu’ expects type ‘long long unsigned int’, but argument 3 has type ‘int64_t’
> lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment_qseq’:
> lib/Bio/DB/Sam.xs:500: warning: operation on ‘seq’ may be undefined
> lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment__qscore’:
> lib/Bio/DB/Sam.xs:514: warning: pointer targets in passing argument 2 of ‘Perl_newSVpv’ differ in signedness
> /usr/lib64/perl5/CORE/proto.h:2210: note: expected ‘const char *’ but argument is of type ‘uint8_t *’
> lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment_aux’:
> lib/Bio/DB/Sam.xs:599: warning: pointer targets in passing argument 2 of ‘strncat’ differ in signedness
> /usr/include/bits/string3.h:151: note: expected ‘const char * __restrict__’ but argument is of type ‘uint8_t *’
> lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment_aux_keys’:
> lib/Bio/DB/Sam.xs:671: warning: pointer targets in passing argument 2 of ‘Perl_newSVpv’ differ in signedness
> /usr/lib64/perl5/CORE/proto.h:2210: note: expected ‘const char *’ but argument is of type ‘uint8_t *’
> lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment_data’:
> lib/Bio/DB/Sam.xs:694: warning: pointer targets in assignment differ in signedness
> lib/Bio/DB/Sam.xs:697: warning: pointer targets in passing argument 2 of ‘Perl_newSVpv’ differ in signedness
> /usr/lib64/perl5/CORE/proto.h:2210: note: expected ‘const char *’ but argument is of type ‘uint8_t *’
> lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Header_view1’:
> lib/Bio/DB/Sam.xs:900: warning: implicit declaration of function ‘bam_view1’
> lib/Bio/DB/Sam.c: In function ‘XS_Bio__DB__Bam__Index_coverage’:
> lib/Bio/DB/Sam.xs:983: warning: unused variable ‘cov’
> lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Pileup_is_refskip’:
> lib/Bio/DB/Sam.xs:1078: error: ‘bam_pileup1_t’ has no member named ‘is_refskip’
> error building lib/Bio/DB/Sam.o from 'lib/Bio/DB/Sam.c' at /usr/local/share/perl5/ExtUtils/CBuilder/Base.pm line 175.
>  LDS/Bio-SamTools-1.27.tar.gz
>  ./Build -- NOT OK
> Running Build test
>  Can't test without successful make
> Running Build install
>  Make had returned bad status, install seems impossible
> Failed during this command:
> LDS/Bio-SamTools-1.27.tar.gz                 : make NO
> 
> Has anyone else seen this problem or have any idea about how to resolve
> it?
> 
> thanks
> Dan Kortschak
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l