dbolser

warn "connecting to link intensity GFF\n";

my $intensities = Bio::DB::SeqFeature::Store->
  new( -adaptor => 'DBI::mysql',
       -dsn => 'dbolser_002:mysql.compbio.dundee.ac.uk',
       -user => 'dbolser',
       -pass => 'abc123',
       -verbose => $verbose,
     );

dbolser

Line 1604 of /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm
    print Dumper $self if !defined $source_tag; exit;


Gives:

$VAR1 = bless( {
                 'dumpdir' => '/tmp',
                 'settings_cache' => {

dbolser

asetaes

dbolser

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)

dbolser

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)

dbolser

# autodetect if openssl is installed
ifeq (${SSLDIR},)
  SSLDIR = /usr/include/openssl
endif
ifeq (${USE_SSL},)
  ifneq ($(wildcard ${SSLDIR}),)
     USE_SSL=1
  endif

dbolser

[dbolser@cricket Bio-BigFile-1.05]$ ./perl Build.PL 
-bash: ./perl: No such file or directory
[dbolser@cricket Bio-BigFile-1.05]$ perl Build.PL 
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-BigFile' version '1.05'
[dbolser@cricket Bio-BigFile-1.05]$ ./Build 
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

dbolser

  CPAN.pm: Going to build L/LD/LDS/Bio-BigFile-1.05.tar.gz

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-BigFile' version '1.05'
Building Bio-BigFile
gcc -I/tmp/funk/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

dbolser

cp Parser/Encodings/x-sjis-jisx0221.enc blib/lib/XML/Parser/Encodings/x-sjis-jisx0221.enc
cp Parser/Style/Stream.pm blib/lib/XML/Parser/Style/Stream.pm
cp Parser/Encodings/iso-8859-5.enc blib/lib/XML/Parser/Encodings/iso-8859-5.enc
make[1]: Entering directory `/homes/dbolser/.cpan/build/XML-Parser-2.40-piAYXa/Expat'
cp Expat.pm ../blib/lib/XML/Parser/Expat.pm
/usr/bin/perl /homes/dbolser/perl5/lib/perl5/ExtUtils/xsubpp -noprototypes -typemap /usr/lib/perl5/5.8.8/ExtUtils/typemap -typemap typemap  Expat.xs > Expat.xsc && mv Expat.xsc Expat.c
gcc -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   -DVERSION=\"2.40\" -DXS_VERSION=\"2.40\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE"   Expat.c
Expat.xs: In function ‘gen

dbolser

sub swapify {
  my $self = shift;
  
  ## Take a copy
  my $swapped = $self->chimera;
  
  ## Swap it
  $swapped->swap;
  
  ## Return the swapified version