[Bioperl-l] install Bio::DB::BigWig ?
Dan Bolser
dan.bolser at gmail.com
Sun Mar 27 18:00:40 UTC 2011
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.
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