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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 ~]$