Skip to content

Instantly share code, notes, and snippets.

@dbolser

dbolser/gist:658585

Created November 1, 2010 17:48
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save dbolser/658585 to your computer and use it in GitHub Desktop.
Save dbolser/658585 to your computer and use it in GitHub Desktop.
Download ZIP
Pasty for deafie
Raw
gistfile1.txt
[dbolser@cricket Compare_To_OPA_SNPs]$
[dbolser@cricket Compare_To_OPA_SNPs]$ cpan
cpan shell -- CPAN exploration and modules installation (v1.9402)
Enter 'h' for help.
cpan[1]> install Bio::DB::Sam
CPAN: Storable loaded ok (v2.21)
Going to read '/homes/dbolser/.cpan/Metadata'
Database was generated on Mon, 01 Nov 2010 02:46:56 GMT
Running install for module 'Bio::DB::Sam'
Running make for L/LD/LDS/Bio-SamTools-1.21.tar.gz
CPAN: Digest::SHA loaded ok (v5.47)
CPAN: Compress::Zlib loaded ok (v2.03)
Checksum for /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-SamTools-1.21.tar.gz ok
CPAN: Archive::Tar loaded ok (v1.62)
Bio-SamTools-1.21
Bio-SamTools-1.21/Changes
Bio-SamTools-1.21/LICENSE
Bio-SamTools-1.21/DISCLAIMER
Bio-SamTools-1.21/Build.PL
Bio-SamTools-1.21/typemap
Bio-SamTools-1.21/META.yml
Bio-SamTools-1.21/README
Bio-SamTools-1.21/MANIFEST
Bio-SamTools-1.21/bin
Bio-SamTools-1.21/bin/bamToGBrowse.pl
Bio-SamTools-1.21/lib
Bio-SamTools-1.21/lib/Bio
Bio-SamTools-1.21/lib/Bio/DB
Bio-SamTools-1.21/lib/Bio/DB/Sam.pm
Bio-SamTools-1.21/lib/Bio/DB/Sam.xs
Bio-SamTools-1.21/lib/Bio/DB/Sam
Bio-SamTools-1.21/lib/Bio/DB/Sam/SamToGBrowse.pm
Bio-SamTools-1.21/lib/Bio/DB/Sam/Constants.pm
Bio-SamTools-1.21/lib/Bio/DB/Sam/Segment.pm
Bio-SamTools-1.21/lib/Bio/DB/Bam
Bio-SamTools-1.21/lib/Bio/DB/Bam/Alignment.pm
Bio-SamTools-1.21/lib/Bio/DB/Bam/Target.pm
Bio-SamTools-1.21/lib/Bio/DB/Bam/FetchIterator.pm
Bio-SamTools-1.21/lib/Bio/DB/Bam/PileupWrapper.pm
Bio-SamTools-1.21/lib/Bio/DB/Bam/AlignWrapper.pm
Bio-SamTools-1.21/lib/Bio/DB/Bam/Query.pm
Bio-SamTools-1.21/lib/Bio/DB/Bam/Pileup.pm
Bio-SamTools-1.21/lib/Bio/DB/Bam/ReadIterator.pm
Bio-SamTools-1.21/t
Bio-SamTools-1.21/t/01sam.t
Bio-SamTools-1.21/t/data
Bio-SamTools-1.21/t/data/ex1.sam.gz
Bio-SamTools-1.21/t/data/ex1.bam
Bio-SamTools-1.21/t/data/00README.txt
Bio-SamTools-1.21/t/data/ex1.fa
CPAN: File::Temp loaded ok (v0.22)
CPAN: YAML loaded ok (v0.71)
---- Unsatisfied dependencies detected during ----
---- LDS/Bio-SamTools-1.21.tar.gz ----
Module::Build [build_requires]
Running make test
Make had some problems, won't test
Delayed until after prerequisites
Running make install
Make had some problems, won't install
Delayed until after prerequisites
Running install for module 'Module::Build'
Running make for D/DA/DAGOLDEN/Module-Build-0.3607.tar.gz
Checksum for /homes/dbolser/.cpan/sources/authors/id/D/DA/DAGOLDEN/Module-Build-0.3607.tar.gz ok
Module-Build-0.3607
Module-Build-0.3607/Changes
Module-Build-0.3607/MANIFEST
Module-Build-0.3607/README
Module-Build-0.3607/LICENSE
Module-Build-0.3607/Build.PL
Module-Build-0.3607/META.yml
Module-Build-0.3607/INSTALL
Module-Build-0.3607/Makefile.PL
Module-Build-0.3607/t
Module-Build-0.3607/t/perl_mb_opt.t
Module-Build-0.3607/t/write_default_maniskip.t
Module-Build-0.3607/t/help.t
Module-Build-0.3607/t/tilde.t
Module-Build-0.3607/t/sample.t
Module-Build-0.3607/t/versions.t
Module-Build-0.3607/t/compat.t
Module-Build-0.3607/t/parents.t
Module-Build-0.3607/t/pod_parser.t
Module-Build-0.3607/t/install_extra_target.t
Module-Build-0.3607/t/manifypods.t
Module-Build-0.3607/t/metadata.t
Module-Build-0.3607/t/PL_files.t
Module-Build-0.3607/t/files.t
Module-Build-0.3607/t/destinations.t
Module-Build-0.3607/t/ppm.t
Module-Build-0.3607/t/par.t
Module-Build-0.3607/t/test_file_exts.t
Module-Build-0.3607/t/resume.t
Module-Build-0.3607/t/xs.t
Module-Build-0.3607/t/install.t
Module-Build-0.3607/t/script_dist.t
Module-Build-0.3607/t/00-compile.t
Module-Build-0.3607/t/notes.t
Module-Build-0.3607/t/runthrough.t
Module-Build-0.3607/t/mymeta.t
Module-Build-0.3607/t/use_tap_harness.t
Module-Build-0.3607/t/test_type.t
Module-Build-0.3607/t/test_types.t
Module-Build-0.3607/t/basic.t
Module-Build-0.3607/t/new_from_context.t
Module-Build-0.3607/t/ext.t
Module-Build-0.3607/t/bundle_inc.t
Module-Build-0.3607/t/README.pod
Module-Build-0.3607/t/add_property.t
Module-Build-0.3607/t/moduleinfo.t
Module-Build-0.3607/t/debug.t
Module-Build-0.3607/t/metadata2.t
Module-Build-0.3607/t/signature.t
Module-Build-0.3607/t/extend.t
Module-Build-0.3607/t/properties
Module-Build-0.3607/t/properties/module_name.t
Module-Build-0.3607/t/properties/share_dir.t
Module-Build-0.3607/t/properties/needs_compiler.t
Module-Build-0.3607/t/lib
Module-Build-0.3607/t/lib/DistGen.pm
Module-Build-0.3607/t/lib/MBTest.pm
Module-Build-0.3607/t/bundled
Module-Build-0.3607/t/bundled/Tie
Module-Build-0.3607/t/bundled/Tie/CPHash.pm
Module-Build-0.3607/t/compat
Module-Build-0.3607/t/compat/exit.t
Module-Build-0.3607/t/actions
Module-Build-0.3607/t/actions/installdeps.t
Module-Build-0.3607/lib
Module-Build-0.3607/lib/Module
Module-Build-0.3607/lib/Module/Build.pm
Module-Build-0.3607/lib/Module/Build
Module-Build-0.3607/lib/Module/Build/PodParser.pm
Module-Build-0.3607/lib/Module/Build/Bundling.pod
Module-Build-0.3607/lib/Module/Build/Base.pm
Module-Build-0.3607/lib/Module/Build/YAML.pm
Module-Build-0.3607/lib/Module/Build/API.pod
Module-Build-0.3607/lib/Module/Build/Version.pm
Module-Build-0.3607/lib/Module/Build/Compat.pm
Module-Build-0.3607/lib/Module/Build/ModuleInfo.pm
Module-Build-0.3607/lib/Module/Build/Cookbook.pm
Module-Build-0.3607/lib/Module/Build/Config.pm
Module-Build-0.3607/lib/Module/Build/PPMMaker.pm
Module-Build-0.3607/lib/Module/Build/Notes.pm
Module-Build-0.3607/lib/Module/Build/Dumper.pm
Module-Build-0.3607/lib/Module/Build/Authoring.pod
Module-Build-0.3607/lib/Module/Build/Platform
Module-Build-0.3607/lib/Module/Build/Platform/darwin.pm
Module-Build-0.3607/lib/Module/Build/Platform/Unix.pm
Module-Build-0.3607/lib/Module/Build/Platform/EBCDIC.pm
Module-Build-0.3607/lib/Module/Build/Platform/aix.pm
Module-Build-0.3607/lib/Module/Build/Platform/MPEiX.pm
Module-Build-0.3607/lib/Module/Build/Platform/Default.pm
Module-Build-0.3607/lib/Module/Build/Platform/MacOS.pm
Module-Build-0.3607/lib/Module/Build/Platform/Windows.pm
Module-Build-0.3607/lib/Module/Build/Platform/Amiga.pm
Module-Build-0.3607/lib/Module/Build/Platform/cygwin.pm
Module-Build-0.3607/lib/Module/Build/Platform/VMS.pm
Module-Build-0.3607/lib/Module/Build/Platform/RiscOS.pm
Module-Build-0.3607/lib/Module/Build/Platform/VOS.pm
Module-Build-0.3607/lib/Module/Build/Platform/os2.pm
Module-Build-0.3607/lib/inc
Module-Build-0.3607/lib/inc/latest.pm
Module-Build-0.3607/lib/inc/latest
Module-Build-0.3607/lib/inc/latest/private.pm
Module-Build-0.3607/contrib
Module-Build-0.3607/contrib/bash_completion.module-build
Module-Build-0.3607/scripts
Module-Build-0.3607/scripts/config_data
CPAN: Module::Build loaded ok (v0.31)
CPAN.pm: Going to build D/DA/DAGOLDEN/Module-Build-0.3607.tar.gz
# running Build.PL
Creating new 'MYMETA.yml' with configuration results
Creating new 'Build' script for 'Module-Build' version '0.3607'
/usr/bin/perl Build --makefile_env_macros 1
Building Module-Build
DAGOLDEN/Module-Build-0.3607.tar.gz
/usr/bin/make -- OK
Running make test
/usr/bin/perl Build --makefile_env_macros 1 test
t/00-compile.t ................. ok
t/PL_files.t ................... ok
t/actions/installdeps.t ........ ok
t/add_property.t ............... ok
t/basic.t ...................... ok
t/bundle_inc.t ................. skipped: $ENV{MB_TEST_EXPERIMENTAL} is not set
t/compat.t ..................... ok -
t/compat/exit.t ................ ok
t/debug.t ...................... ok
t/destinations.t ............... ok
t/ext.t ........................ ok
t/extend.t ..................... ok
t/files.t ...................... ok
t/help.t ....................... ok
t/install.t .................... ok
t/install_extra_target.t ....... ok
t/manifypods.t ................. ok
t/metadata.t ................... ok
t/metadata2.t .................. ok
t/moduleinfo.t ................. ok
t/mymeta.t ..................... ok
t/new_from_context.t ........... ok
t/notes.t ...................... ok
t/par.t ........................ skipped: PAR::Dist 0.17 or up not installed to check .par's.
t/parents.t .................... ok
t/perl_mb_opt.t ................ ok
t/pod_parser.t ................. ok
t/ppm.t ........................ ok
t/properties/module_name.t ..... ok
t/properties/needs_compiler.t .. ok
t/properties/share_dir.t ....... ok
t/resume.t ..................... ok
t/runthrough.t ................. ok
t/sample.t ..................... ok
t/script_dist.t ................ ok
t/signature.t .................. skipped: $ENV{TEST_SIGNATURE} is not set
t/test_file_exts.t ............. ok
t/test_type.t .................. ok
t/test_types.t ................. ok
t/tilde.t ...................... ok
t/use_tap_harness.t ............ ok
t/versions.t ................... ok
t/write_default_maniskip.t ..... ok
t/xs.t ......................... ok
All tests successful.
Files=44, Tests=1161, 62 wallclock secs ( 0.39 usr 0.07 sys + 44.33 cusr 8.52 csys = 53.31 CPU)
Result: PASS
DAGOLDEN/Module-Build-0.3607.tar.gz
/usr/bin/make test -- OK
Running make install
D/DA/DAGOLDEN/Module-Build-0.3607.tar.gz is just needed temporarily during building or testing. Do you want to install it permanently? [yes] yes
Not installing because is only 'build_requires'
Running make for L/LD/LDS/Bio-SamTools-1.21.tar.gz
Prepending /homes/dbolser/.cpan/build/Module-Build-0.3607-CUrpsG/blib/arch /homes/dbolser/.cpan/build/Module-Build-0.3607-CUrpsG/blib/lib to PERL5LIB for 'get'
CPAN: Time::HiRes loaded ok (v1.9717)
Prepending /homes/dbolser/.cpan/build/Module-Build-0.3607-CUrpsG/blib/arch /homes/dbolser/.cpan/build/Module-Build-0.3607-CUrpsG/blib/lib to PERL5LIB for 'make'
CPAN.pm: Going to build L/LD/LDS/Bio-SamTools-1.21.tar.gz
This module requires samtools 0.1.4 or higher (samtools.sourceforge.net).
Please enter the location of the bam.h and compiled libbam.a files: /homes/dbolser/build/src/samtools-0.1.9
Found /homes/dbolser/build/src/samtools-0.1.9/bam.h and /homes/dbolser/build/src/samtools-0.1.9/libbam.a.
Creating new 'MYMETA.yml' with configuration results
Creating new 'Build' script for 'Bio-SamTools' version '1.21'
Building Bio-SamTools
gcc -I/homes/dbolser/build/src/samtools-0.1.9 -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE -DXS_VERSION="1.21" -DVERSION="1.21" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wformat=0 -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -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:105: warning: unused variable ‘pileup_obj’
lib/Bio/DB/Sam.c: In function ‘XS_Bio__DB__Bam_open’:
lib/Bio/DB/Sam.c:514: warning: unused variable ‘packname’
lib/Bio/DB/Sam.c: In function ‘XS_Bio__DB__Bam_index_build’:
lib/Bio/DB/Sam.c:572: warning: unused variable ‘packname’
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam_sort_core’:
lib/Bio/DB/Sam.xs:304: warning: implicit declaration of function ‘bam_sort_core’
lib/Bio/DB/Sam.c:596: warning: unused variable ‘packname’
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam_tell’:
lib/Bio/DB/Sam.xs:346: warning: ISO C90 forbids mixed declarations and code
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment_qseq’:
lib/Bio/DB/Sam.xs:498: 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:512: warning: pointer targets in passing argument 2 of ‘Perl_newSVpv’ differ in signedness
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment_aux’:
lib/Bio/DB/Sam.xs:573: warning: ISO C90 forbids mixed declarations and code
lib/Bio/DB/Sam.xs:597: warning: pointer targets in passing argument 2 of ‘__builtin___strncat_chk’ differ in signedness
lib/Bio/DB/Sam.xs:597: warning: pointer targets in passing argument 2 of ‘__strncat_ichk’ differ in signedness
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment_aux_keys’:
lib/Bio/DB/Sam.xs:669: warning: pointer targets in passing argument 2 of ‘Perl_newSVpv’ differ in signedness
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment_data’:
lib/Bio/DB/Sam.xs:692: warning: pointer targets in assignment differ in signedness
lib/Bio/DB/Sam.xs:695: warning: pointer targets in passing argument 2 of ‘Perl_newSVpv’ differ in signedness
lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Header_view1’:
lib/Bio/DB/Sam.xs:898: 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:981: warning: unused variable ‘cov’
lib/Bio/DB/Sam.c: In function ‘invoke_pileup_callback_fun’:
lib/Bio/DB/Sam.xs:150: warning: control reaches end of non-void function
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/Sam/Sam.bs')
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib -o blib/arch/auto/Bio/DB/Sam/Sam.so lib/Bio/DB/Sam.o -L/homes/dbolser/build/src/samtools-0.1.9 -lbam -lz
LDS/Bio-SamTools-1.21.tar.gz
./Build -- OK
Prepending /homes/dbolser/.cpan/build/Module-Build-0.3607-CUrpsG/blib/arch /homes/dbolser/.cpan/build/Module-Build-0.3607-CUrpsG/blib/lib to PERL5LIB for 'test'
Running Build test
t/01sam.t .. 1/104 [fai_load] build FASTA index.
t/01sam.t .. ok
All tests successful.
Files=1, Tests=104, 1 wallclock secs ( 0.03 usr 0.01 sys + 1.15 cusr 0.13 csys = 1.32 CPU)
Result: PASS
LDS/Bio-SamTools-1.21.tar.gz
./Build test -- OK
Running Build install
Prepending /homes/dbolser/.cpan/build/Bio-SamTools-1.21-BTX9wY/blib/arch /homes/dbolser/.cpan/build/Bio-SamTools-1.21-BTX9wY/blib/lib /homes/dbolser/.cpan/build/Module-Build-0.3607-CUrpsG/blib/arch /homes/dbolser/.cpan/build/Module-Build-0.3607-CUrpsG/blib/lib to PERL5LIB for 'install'
Building Bio-SamTools
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /local/Scratch/dbolser/perl5/lib/perl5/i386-linux-thread-multi/auto/Bio/DB/Sam/Sam.so
LDS/Bio-SamTools-1.21.tar.gz
./Build install -- OK
Failed during this command:
DAGOLDEN/Module-Build-0.3607.tar.gz : install NO -- is only 'build_requires'
cpan[2]>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment