[Bioperl-l] install Bio::DB::BigWig ?
Lincoln Stein
lincoln.stein at gmail.com
Mon Mar 28 17:26:20 EDT 2011
Hi Dan,
There are two problems that I can see. One is a series of compiler warnings
when compiling the Perl .XS interface file. These are likely nothing to
worry about, but I should fix them. What versions of Perl and gcc do you
have installed? I don't see them when I compile on my system.
The second issue is that the SSL library is not being linked in. Previously
there was no dependency on SSL, but Jim may recently have added this to the
BigWig library in order to allow it to read bigwig files from https servers.
I see that you added a -lssl to Build.PL; does this make the tests work
again?
Lincoln
On Sun, Mar 27, 2011 at 2:00 PM, 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.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
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