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Id: 105418
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Queue: Bio-SamTools

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Requestors: shokin [...] carnegiescience.edu
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Subject: Compile error under CentOS 6.6
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I'm hitting a compile error when trying to install Bio::DB::Sam from CPAN. This is under CentOS 6.6 with all of the appropriate yum-installed packages. I grabbed samtools and htslib from github and compiled them locally. Here is the compile/error stream: CPAN: Storable loaded ok (v2.20) Going to read '/root/.cpan/Metadata' Database was generated on Mon, 22 Jun 2015 23:53:33 GMT Running install for module 'Bio::DB::Sam' CPAN: YAML loaded ok (v0.70) Running make for L/LD/LDS/Bio-SamTools-1.41.tar.gz CPAN: Digest::SHA loaded ok (v5.47) CPAN: Compress::Zlib loaded ok (v2.021) Checksum for /root/.cpan/sources/authors/id/L/LD/LDS/Bio-SamTools-1.41.tar.gz ok CPAN: Archive::Tar loaded ok (v1.58) Bio-SamTools-1.41 Bio-SamTools-1.41/DISCLAIMER Bio-SamTools-1.41/README Bio-SamTools-1.41/MANIFEST Bio-SamTools-1.41/META.json Bio-SamTools-1.41/Build.PL Bio-SamTools-1.41/INSTALL.pl Bio-SamTools-1.41/LICENSE Bio-SamTools-1.41/typemap Bio-SamTools-1.41/META.yml Bio-SamTools-1.41/Changes Bio-SamTools-1.41/bin Bio-SamTools-1.41/bin/bamToGBrowse.pl Bio-SamTools-1.41/bin/chrom_sizes.pl Bio-SamTools-1.41/bin/genomeCoverageBed.pl Bio-SamTools-1.41/t Bio-SamTools-1.41/t/01sam.t Bio-SamTools-1.41/t/data Bio-SamTools-1.41/t/data/dm3_3R_4766911_4767130.sam.bam Bio-SamTools-1.41/t/data/00README.txt Bio-SamTools-1.41/t/data/dm3_3R_4766911_4767130.sam Bio-SamTools-1.41/t/data/ex1.fa Bio-SamTools-1.41/t/data/ex1.bam Bio-SamTools-1.41/t/data/ex1.sam.gz Bio-SamTools-1.41/t/data/dm3_3R_4766911_4767130.sam.sorted.bam Bio-SamTools-1.41/lib Bio-SamTools-1.41/lib/Bio Bio-SamTools-1.41/lib/Bio/DB Bio-SamTools-1.41/lib/Bio/DB/Sam.pm Bio-SamTools-1.41/lib/Bio/DB/Sam.xs Bio-SamTools-1.41/lib/Bio/DB/Sam Bio-SamTools-1.41/lib/Bio/DB/Sam/Constants.pm Bio-SamTools-1.41/lib/Bio/DB/Sam/SamToGBrowse.pm Bio-SamTools-1.41/lib/Bio/DB/Sam/Segment.pm Bio-SamTools-1.41/lib/Bio/DB/Bam Bio-SamTools-1.41/lib/Bio/DB/Bam/Pileup.pm Bio-SamTools-1.41/lib/Bio/DB/Bam/AlignWrapper.pm Bio-SamTools-1.41/lib/Bio/DB/Bam/FetchIterator.pm Bio-SamTools-1.41/lib/Bio/DB/Bam/Alignment.pm Bio-SamTools-1.41/lib/Bio/DB/Bam/ReadIterator.pm Bio-SamTools-1.41/lib/Bio/DB/Bam/Target.pm Bio-SamTools-1.41/lib/Bio/DB/Bam/Query.pm Bio-SamTools-1.41/lib/Bio/DB/Bam/PileupWrapper.pm Bio-SamTools-1.41/c_bin Bio-SamTools-1.41/c_bin/makefile Bio-SamTools-1.41/c_bin/bam2bedgraph.c CPAN: File::Temp loaded ok (v0.22) CPAN: Time::HiRes loaded ok (v1.9726) CPAN.pm: Going to build L/LD/LDS/Bio-SamTools-1.41.tar.gz This module requires samtools 0.1.10 or higher (samtools.sourceforge.net). Please enter the location of the bam.h and compiled libbam.a files: /home/hokins/samtools Found /home/hokins/samtools/bam.h and /home/hokins/samtools/libbam.a. Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-SamTools' version '1.41' CPAN: Module::Build loaded ok (v0.4214) Building Bio-SamTools gcc -I/home/hokins/samtools -Ic_bin -I/usr/lib64/perl5/CORE -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 c_bin/bam2bedgraph.o c_bin/bam2bedgraph.c gcc -I/home/hokins/samtools -Ic_bin -I/usr/lib64/perl5/CORE -DXS_VERSION="1.41" -DVERSION="1.41" -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:118: warning: unused variable ‘pileups’ lib/Bio/DB/Sam.xs:116: warning: unused variable ‘pileup_obj’ lib/Bio/DB/Sam.c: In function ‘XS_Bio__DB__Bam_open’: lib/Bio/DB/Sam.c:563: warning: unused variable ‘packname’ lib/Bio/DB/Sam.c: In function ‘XS_Bio__DB__Bam_index_build’: lib/Bio/DB/Sam.c:623: warning: unused variable ‘packname’ lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam_sort_core’: lib/Bio/DB/Sam.xs:324: warning: implicit declaration of function ‘bam_sort_core’ lib/Bio/DB/Sam.c:647: warning: unused variable ‘packname’ lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment_qseq’: lib/Bio/DB/Sam.xs:518: 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:532: 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_l_aux’: lib/Bio/DB/Sam.xs:575: error: ‘bam1_t’ has no member named ‘l_aux’ lib/Bio/DB/Sam.xs:576: error: ‘bam1_t’ has no member named ‘l_aux’ lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment_aux’: lib/Bio/DB/Sam.xs:615: warning: pointer targets in passing argument 2 of ‘strncat’ differ in signedness /usr/include/bits/string3.h:149: 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:687: 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:710: warning: pointer targets in assignment differ in signedness lib/Bio/DB/Sam.xs:713: 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.c: In function ‘XS_Bio__DB__Bam__Index_coverage’: lib/Bio/DB/Sam.xs:1001: warning: unused variable ‘cov’ error building lib/Bio/DB/Sam.o from 'lib/Bio/DB/Sam.c' at /usr/share/perl5/ExtUtils/CBuilder/Base.pm line 112. LDS/Bio-SamTools-1.41.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 [hokins@centos6 ~]$
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What version of SAMtools do you have installed? AFAIK, newer versions of SAMtools are not compatible with Bio::DB::Sam.
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I've tried many versions. This particular bug was filed after trying with: Version: 1.2-83-g39a35af (using htslib 1.2.1-122-g53a7528) But I also tried with: Version: 1.0 (using htslib 1.2.1-122-g53a7528) Version: 1.2 (using htslib 1.2.1) It's definitely an incompatibility with some stock CentOS6.6 Perl (?) installs - a colleague is running CentOS6.6 but installed all the Perl on his server from CPAN and Bio::DB::Sam compiled OK. (I found this out after filing the bug.) So perhaps this doesn't warrant a lot of research. This colleague said that the reason he installs all Perl from CPAN is that there are in fact incompatibilities with CentOS6.6 distro versions. On 08/20/2015 07:24 AM, Dan Bolser via RT wrote: Show quoted text
> <URL: https://rt.cpan.org/Ticket/Display.html?id=105418 > > > What version of SAMtools do you have installed? AFAIK, newer versions of SAMtools are not compatible with Bio::DB::Sam. >


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