and the test passed (03.render.t) which was hanging before. However now
> Hi Frederic,
>
> Could you install this version of Bio::Graphics and let me know if it
> improves things?
>
> There is a bug in libgd's ImageFillToBorder() function which triggers on
> 64 bit systems. There is a patch floating around on the Internet, but it
> will be a pain to apply. So I've eliminated calls to the function in
> this version of Bio::Graphics.
>
> Lincoln
>
>
>
> On Tue, Jun 23, 2009 at 1:33 PM, <
frederic.potier@...
> <mailto:
frederic.potier@...>> wrote:
>
>
> Hi Lincoln,
> I did not had time yet to test your modifications. (just back from
> long week end ;))
> So to answer to your question, we are indeed running gbrowse on 64
> bit machine (RHEL 5).
>
> so here is the output from perl :
> perl -V
> Summary of my perl5 (revision 5 version 10 subversion 0) configuration:
> Platform:
> osname=linux, osvers=2.6.18-128.1.1.el5, archname=x86_64-linux
> uname='linux vmtemplate1.be.bayercropscience 2.6.18-128.1.1.el5
> #1 smp mon jan 26 13:58:24 est 2009 x86_64 x86_64 x86_64 gnulinux '
> config_args=''
> hint=recommended, useposix=true, d_sigaction=define
> useithreads=undef, usemultiplicity=undef
> useperlio=define, d_sfio=undef, uselargefiles=define,
> usesocks=undef
> use64bitint=define, use64bitall=define, uselongdouble=undef
> usemymalloc=n, bincompat5005=undef
> Compiler:
> cc='gcc', ccflags ='-fPIC -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm',
> optimize='-O2',
> cppflags='-fPIC -I/usr/include/gdbm'
> ccversion='', gccversion='4.1.2 20080704 (Red Hat 4.1.2-44)',
> gccosandvers=''
> intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
> d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
> ivtype='long', ivsize=8, nvtype='double', nvsize=8,
> Off_t='off_t', lseeksize=8
> alignbytes=8, prototype=define
> Linker and Libraries:
> ld='gcc', ldflags =' -L/usr/local/lib'
> libpth=/usr/local/lib /lib /usr/lib /lib64 /usr/lib64
> /usr/local/lib64
> libs=-lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc
> perllibs=-lnsl -ldl -lm -lcrypt -lutil -lc
> libc=/lib/libc-2.5.so <
http://libc-2.5.so>, so=so,
> useshrplib=false, libperl=libperl.a
> gnulibc_version='2.5'
> Dynamic Linking:
> dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
> cccdlflags='-fPIC', lddlflags='-shared -O2 -L/usr/local/lib'
>
>
> Characteristics of this binary (from libperl):
> Compile-time options: PERL_DONT_CREATE_GVSV PERL_MALLOC_WRAP
> USE_64_BIT_ALL
> USE_64_BIT_INT USE_LARGE_FILES USE_PERLIO
> Built under linux
> Compiled at Apr 1 2009 16:36:03
> %ENV:
> PERL5LIB="/tools/bioinfo/bioim_modules:"
> @INC:
> /tools/bioinfo/bioim_modules
> /usr/local/lib/perl5/5.10.0/x86_64-linux
> /usr/local/lib/perl5/5.10.0
> /usr/local/lib/perl5/site_perl/5.10.0/x86_64-linux
> /usr/local/lib/perl5/site_perl/5.10.0
>
> If you need me to test something I'll try to do it today before
> living work.
>
> thanks a lot
>
> Best Regards / Mit freundlichen Grüßen / Cordialement
> *
> F. POTIER*
>
> *BioScience
> Genomics Data Platform Team *
>
> Technologiepark 38, B-9052 Zwijnaarde
> +32 (0)9 243 04 30
> +32 (0)9 224 06 94
>
frederic.potier@...
> <mailto:
frederic.potier@...>
>
http://bioim.bioscience.bayercropscience>
>
>
>
>
>
> *Lincoln Stein <
lincoln.stein@...
> <mailto:
lincoln.stein@...>>*
>
> 06/23/2009 02:29 PM
>
>
> To
> Frederic Potier <
frederic.potier@...
> <mailto:
frederic.potier@...>>
> cc
>
> Erick Antezana <
erick.antezana@...
> <mailto:
erick.antezana@...>>
> Subject
> Re: off until next thursday
>
>
>
>
>
>
>
>
> Hi Frederic,
>
> I have a working hypothesis that the crash only occurs on 64-bit
> platforms. Are you running on a 64 bit machine? Could you send me
> the output of perl -V?
>
> Thanks,
>
> Lincoln
>
> On Fri, Jun 19, 2009 at 4:28 PM, Erick Antezana
> <
_erick.antezana@... <mailto:
erick.antezana@...>> wrote:
> Hi Lincoln,
>
> I just wanted to let you know that I will be on the road during
> the coming days. I am back on business next Thursday 25. However, in
> the meantime, a colleague of mine (CC-ed) could continue the
> debugging process and tracking down the issues related to the
> visualisation of karyotypes.
>
> cheers,
> Erick
>
>
>
> --
> 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@...
> <mailto:
Renata.Musa@...>>
>
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>
>
>
> --
> 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@...
> <mailto:
Renata.Musa@...>>
>
>
> ------------------------------------------------------------------------
>
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Bio-Graphics-1.97.tar.gz (850K) 
