[Bioperl-l] install Bio::DB::BigWig ?

[Dan Bolser]

--- Build.PL~   2011-03-14 20:27:57.000000000 +0000
+++ Build.PL    2011-03-28 18:06:45.503757000 +0100
@@ -16,7 +16,7 @@
     dist_abstract      => "Manipulate Jim Kent's BigWig and BigBed
index files for genomic features.",
     license            => 'perl',
     include_dirs       => [$jk_include],
-    extra_linker_flags => ["$jk_lib/$LibFile",'-lz'],
+    extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl'],

     extra_compiler_flags=>[
        # turn off warnings originating in Perl's Newx* calls

On 27 March 2011 19:00, Dan Bolser <dan.bolser at gmail.com> wrote:
> Hello,
>
> I'm trying to get Bio::DB::BigWig installed again, this time on a different box.
>
> I installed kent from git as described here:
> http://genome.ucsc.edu/admin/git.html
>
>
> I made the following changes, similar to those described previously:
>
> git diff
> diff --git a/src/inc/common.mk b/src/inc/common.mk
> index c7fc557..5187901 100644
> --- a/src/inc/common.mk
> +++ b/src/inc/common.mk
> @@ -3,7 +3,7 @@ CC=gcc
>  ifeq (${COPT},)
>     COPT=-O -g
>  endif
> -CFLAGS=
> +CFLAGS=-fPIC
>  HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> -DMACHTYPE_${MACHTYPE}
>  HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc
> -I../../../../../inc
>
> diff --git a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> index fa2292b..acb97d2 100644
> --- a/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> +++ b/src/utils/bedRemoveOverlap/bedRemoveOverlap.c
> @@ -68,7 +68,7 @@ while (lineFileNext(lf, &line, &lineSize))
>     /* Parse current line. */
>     wordCount = chopLine(line, row);
>     if (wordCount == ArraySize(row))
> -         errAbort("Too many fields (%d max is %lu) line %d of %s",
> wordCount, ArraySize(row),
> +         errAbort("Too many fields (%d max is %u) line %d of %s",
> wordCount, ArraySize(row),
>             lf->lineIx, lf->fileName);
>     char *chrom = row[0];
>     unsigned int start = lineFileNeedNum(lf, row, 1);
>
>
> After setting MACHTYPE=i686, MYSQLLIBS=/usr/lib/mysql/libmysqlclient.a
> -lz, and MYSQLINC=/usr/include/mysql, everything seemed to build
> correctly after typing 'make' in kent/src (should I be building it
> differently?)
>
>
>
> Now when I try to install Bio::DB::BigWig via cpan, things look like this:
>
> cpan
>
> cpan shell -- CPAN exploration and modules installation (v1.9600)
> Enter 'h' for help.
>
> cpan[1]> install Bio::DB::BigWig
> CPAN: Storable loaded ok (v2.25)
> Going to read '/homes/dbolser/.cpan/Metadata'
>  Database was generated on Sun, 27 Mar 2011 01:38:43 GMT
> Running install for module 'Bio::DB::BigWig'
> Running make for L/LD/LDS/Bio-BigFile-1.05.tar.gz
> CPAN: Digest::SHA loaded ok (v5.61)
> CPAN: Compress::Zlib loaded ok (v2.03)
> Checksum for /homes/dbolser/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.05.tar.gz
> ok
> CPAN: Archive::Tar loaded ok (v1.76)
> Bio-BigFile-1.05
> Bio-BigFile-1.05/Changes
> Bio-BigFile-1.05/LICENSE
> Bio-BigFile-1.05/DISCLAIMER
> Bio-BigFile-1.05/Build.PL
> Bio-BigFile-1.05/typemap
> Bio-BigFile-1.05/META.yml
> Bio-BigFile-1.05/README
> Bio-BigFile-1.05/MANIFEST
> Bio-BigFile-1.05/ExampleData
> Bio-BigFile-1.05/ExampleData/dpy-27-variable.bw
> Bio-BigFile-1.05/ExampleData/hg18.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bb
> Bio-BigFile-1.05/ExampleData/WS180.chrom.sizes
> Bio-BigFile-1.05/ExampleData/refSeqTest.flat.bed
> Bio-BigFile-1.05/ExampleData/refSeqTest.as
> Bio-BigFile-1.05/ExampleData/dpy-27-variable-trunk.wig.gz
> Bio-BigFile-1.05/bin
> Bio-BigFile-1.05/bin/bigWigToWig.pl
> Bio-BigFile-1.05/bin/wigToBigWig.pl
> Bio-BigFile-1.05/bin/index_bigwigset.pl
> Bio-BigFile-1.05/lib
> Bio-BigFile-1.05/lib/Bio
> Bio-BigFile-1.05/lib/Bio/DB
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWigSet.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile.xs
> Bio-BigFile-1.05/lib/Bio/DB/BigBed.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigWig.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Iterators.pm
> Bio-BigFile-1.05/lib/Bio/DB/BigFile/Constants.pm
> Bio-BigFile-1.05/t
> Bio-BigFile-1.05/t/02.bigbed.t
> Bio-BigFile-1.05/t/03.bigwig_high.t
> Bio-BigFile-1.05/t/04.bigbed_high.t
> Bio-BigFile-1.05/t/05.bigwig_set.t
> /bin/tar: Read 9216 bytes from -
> Bio-BigFile-1.05/t/01.bigwig.t
> Bio-BigFile-1.05/patches
> Bio-BigFile-1.05/patches/kent_src_patch_macosx.diff
> CPAN: File::Temp loaded ok (v0.22)
> CPAN: Parse::CPAN::Meta loaded ok (v1.4401)
> CPAN: CPAN::Meta loaded ok (v2.110580)
> CPAN: Module::CoreList loaded ok (v2.46)
> CPAN: Time::HiRes loaded ok (v1.9717)
>
>  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz
>
>
> This module requires the compiled jkweb.a library from Jim Kent's source tree.
> If you haven't already done so, please download the source from
> http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
> contents of the "kent/src/lib" subdirectory as directed in the README. Then
> enter the location of the "kent/src" subdirectory at the prompt below.
> To prevent
> this message from appearing in the future, set the environment
> variable KENT_SRC
> to point to the "kent/src" subdirectory.
>
> Please enter the location of Kent source tree: /homes/dbolser/build/src/kent/src
>
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'Bio-BigFile' version '1.05'
> Building Bio-BigFile
> gcc -I/homes/dbolser/build/src/kent/src/inc
> -I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE
> -DXS_VERSION="1.05" -DVERSION="1.05" -fPIC -Wformat=0 -DMACHTYPE_i686
> -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/BigFile.o
> lib/Bio/DB/BigFile.c
> lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigWigIntervalQuery’:
> lib/Bio/DB/BigFile.xs:172: warning: operation on ‘list’ may be undefined
> lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigWigSummaryArray’:
> lib/Bio/DB/BigFile.xs:193: warning: operation on ‘values’ may be undefined
> lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigBedSummaryArray’:
> lib/Bio/DB/BigFile.xs:252: warning: operation on ‘values’ may be undefined
> lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigWigSummary’:
> lib/Bio/DB/BigFile.xs:296: warning: operation on ‘summary’ may be undefined
> lib/Bio/DB/BigFile.xs:302: warning: operation on ‘summaryList’ may be undefined
> lib/Bio/DB/BigFile.xs:290: warning: unused variable ‘i’
> lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigBedSummary’:
> lib/Bio/DB/BigFile.xs:326: warning: operation on ‘summary’ may be undefined
> lib/Bio/DB/BigFile.xs:332: warning: operation on ‘summaryList’ may be undefined
> lib/Bio/DB/BigFile.xs:320: warning: unused variable ‘i’
> lib/Bio/DB/BigFile.xs: In function
> ‘XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended’:
> lib/Bio/DB/BigFile.xs:358: warning: operation on ‘summary’ may be undefined
> lib/Bio/DB/BigFile.xs:354: warning: unused variable ‘summaryList’
> lib/Bio/DB/BigFile.xs: In function
> ‘XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended’:
> lib/Bio/DB/BigFile.xs:395: warning: operation on ‘summary’ may be undefined
> lib/Bio/DB/BigFile.xs:391: warning: unused variable ‘summaryList’
> lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_chromList’:
> lib/Bio/DB/BigFile.xs:424: warning: operation on ‘RETVAL’ may be undefined
> lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigBedIntervalQuery’:
> lib/Bio/DB/BigFile.xs:450: warning: operation on ‘list’ may be undefined
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.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/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> /homes/dbolser/build/src/kent/src/lib/i686/jkweb.a -lz
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build -- OK
> CPAN: YAML loaded ok (v0.72)
> Running Build test
> t/01.bigwig.t ....... Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/01.bigwig.t line 28
> Compilation failed in require at t/01.bigwig.t line 28.
> BEGIN failed--compilation aborted at t/01.bigwig.t line 28.
> t/01.bigwig.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 29/29 subtests
> t/02.bigbed.t ....... Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at t/02.bigbed.t line 28
> Compilation failed in require at t/02.bigbed.t line 28.
> BEGIN failed--compilation aborted at t/02.bigbed.t line 28.
> t/02.bigbed.t ....... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 15/15 subtests
> t/03.bigwig_high.t .. Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at t/03.bigwig_high.t line 28.
> BEGIN failed--compilation aborted at t/03.bigwig_high.t line 28.
> t/03.bigwig_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 32/32 subtests
> t/04.bigbed_high.t .. Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigBed.pm
> line 7.
> Compilation failed in require at t/04.bigbed_high.t line 28.
> BEGIN failed--compilation aborted at t/04.bigbed_high.t line 28.
> t/04.bigbed_high.t .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 35/35 subtests
> t/05.bigwig_set.t ... Can't load
> '/homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so'
> for module Bio::DB::BigFile:
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so:
> undefined symbol: SSL_library_init at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230.
>  at /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWig.pm
> line 7.
> Compilation failed in require at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> BEGIN failed--compilation aborted at
> /homes/dbolser/.cpan/build/Bio-BigFile-1.05-RcWq8X/t/../lib/Bio/DB/BigWigSet.pm
> line 177.
> Compilation failed in require at t/05.bigwig_set.t line 19.
> BEGIN failed--compilation aborted at t/05.bigwig_set.t line 19.
> t/05.bigwig_set.t ... Dubious, test returned 2 (wstat 512, 0x200)
> No subtests run
>
> Test Summary Report
> -------------------
> t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 29 tests but ran 0.
> t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 32 tests but ran 0.
> t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 35 tests but ran 0.
> t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: No plan found in TAP output
> Files=5, Tests=0,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr
> 0.11 csys =  1.09 CPU)
> Result: FAIL
> Failed 5/5 test programs. 0/0 subtests failed.
>  LDS/Bio-BigFile-1.05.tar.gz
>  ./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
>  reports LDS/Bio-BigFile-1.05.tar.gz
> Running Build install
>  make test had returned bad status, won't install without force
> Failed during this command:
>  LDS/Bio-BigFile-1.05.tar.gz                  : make_test NO
>
> cpan[2]>
>
>
>
>
>
>
> Any hints?
>
> Cheers,
> Dan.
>