[Bioperl-l] Budle::BioPerl dependency issues

Lincoln Stein lincoln.stein at gmail.com
Sun Nov 19 10:54:11 EST 2006


That's very odd. gd.0.28 should install gdlib-config, and the existence of
this executable should inhibit the interactive questions. Could you see if
there's a gdlib-config executable installed on your system?

Lincoln

On 11/18/06, gang wu <gwu at molbio.mgh.harvard.edu> wrote:
>
> Lincoln,
> Thanks for your message. I have gd-2.0.28-4.4E.1 and
> gd-devel-2.0.28-4.4E.1 installed under Redhat AS 4 for AMD/EM64T.
> Attached is the output.
>
> Gang
>
> ==================================================
> [root at elegans GD-2.35]# perl Makefile.PL
> NOTICE: This module requires libgd 2.0.28 or higher.
>
>         If you are using Math::Trig 1.01 or lower, it has a bug that
>         causes a "prerequisite not found" warning to be issued.  You may
>         safely ignore this warning.
>
>         Type perl Makefile.PL -h for command-line option summary
>
>
> Where is libgd installed? [/usr/lib]
>
> Please choose the features that match how libgd was built:
> Build JPEG support? [y]
> Build PNG support? [y]
> Build FreeType support? [y]
> Build GIF support? [y]
> Build support for animated GIFs? [y]
> Build XPM support? [y]
>
> If you experience compile problems, please check the @INC, @LIBPATH and
> @LIBS
> arrays defined in Makefile.PL and manually adjust, if necessary.
>
> Checking if your kit is complete...
> Looks good
> Writing Makefile for GD
> [root at elegans GD-2.35]# make
> cp GD/Polyline.pm blib/lib/GD/Polyline.pm
> cp qd.pl blib/lib/qd.pl
> cp GD/Image.pm blib/lib/GD/Image.pm
> cp GD.pm blib/lib/GD.pm
> AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD)
> cp GD/Simple.pm blib/lib/GD/Simple.pm
> cp GD/Polygon.pm blib/lib/GD/Polygon.pm
> /usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp  -typemap
> /usr/lib/perl5/5.8.5/ExtUtils/typemap -typemap typemap  GD.xs > GD.xsc
> && mv GD.xsc GD.c
> gcc -c  -I/usr/include -I/usr/include/gd -D_REENTRANT -D_GNU_SOURCE
> -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include
> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
> -pipe -m64   -DVERSION=\"2.35\" -DXS_VERSION=\"2.35\" -fPIC
> "-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE"  -DHAVE_JPEG
> -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF GD.c
> GD.xs: In function `XS_GD__Image_STORABLE_thaw':
> GD.xs:923: warning: cast from pointer to integer of different size
> GD.xs: In function `XS_GD__Image_gifanimbegin':
> GD.xs:990: warning: cast to pointer from integer of different size
> GD.xs: In function `XS_GD__Image_gifanimadd':
> GD.xs:1015: warning: cast to pointer from integer of different size
> GD.xs: In function `XS_GD__Image_gifanimend':
> GD.xs:1034: warning: cast to pointer from integer of different size
> Running Mkbootstrap for GD ()
> chmod 644 GD.bs
> rm -f blib/arch/auto/GD/GD.so
> gcc  -shared GD.o  -o blib/arch/auto/GD/GD.so   -L/usr/lib/X11
> -L/usr/X11R6/lib -L/usr/lib -L/usr/lib/X11 -L/usr/X11R6/lib64
> -L/usr/lib64 -lgd -lfreetype -ljpeg -lpng -lz -lm -lX11 -lXpm
> /usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz
> /usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz
> /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
> /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm
> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when
> searching for -lX11
> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when
> searching for -lX11
> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.so when
> searching for -lXpm
> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXpm.a when
> searching for -lXpm
> /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
> /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc
> chmod 755 blib/arch/auto/GD/GD.so
> cp GD.bs blib/arch/auto/GD/GD.bs
> chmod 644 blib/arch/auto/GD/GD.bs
> cp bdf_scripts/bdf2gdfont.pl blib/script/bdf2gdfont.pl
> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)"
> blib/script/bdf2gdfont.pl
> Manifying blib/man1/bdf2gdfont.pl.1
> Manifying blib/man3/GD::Polyline.3pm
> Manifying blib/man3/GD::Image.3pm
> Manifying blib/man3/GD::Simple.3pm
> Manifying blib/man3/GD.3pm
> Manifying blib/man3/GD::Polygon.3pm
> [root at elegans GD-2.35]# make test
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD:
> ./blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at
> /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230.
> at t/GD.t line 14
> Compilation failed in require at t/GD.t line 14.
> BEGIN failed--compilation aborted at t/GD.t line 14.
> t/GD..........dubious
>
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-12
>         Failed 12/12 tests, 0.00% okay
> t/Polyline....Can't load
> '/root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so' for module GD:
> /root/.cpan/build/GD-2.35/blib/arch/auto/GD/GD.so: undefined symbol:
> gdImageGifAnimAddPtr at
> /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230.
> at /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45
> Compilation failed in require at
> /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45.
> BEGIN failed--compilation aborted at
> /root/.cpan/build/GD-2.35/blib/lib/GD/Polyline.pm line 45.
> Compilation failed in require at t/Polyline.t line 10.
> BEGIN failed--compilation aborted at t/Polyline.t line 10.
> t/Polyline....dubious
>
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED test 1
>         Failed 1/1 tests, 0.00% okay
> Failed Test  Stat Wstat Total Fail  Failed  List of Failed
>
> -------------------------------------------------------------------------------
> t/GD.t        255 65280    12   23 191.67%  1-12
> t/Polyline.t  255 65280     1    2 200.00%  1
> Failed 2/2 test scripts, 0.00% okay. 13/13 subtests failed, 0.00% okay.
> make: *** [test_dynamic] Error 255
> [root at elegans GD-2.35]#
> ===========================================================
>
> Lincoln Stein wrote:
> > What version of libgd do you have installed? With recent versions of
> > libgd (more recent than two years old) you will not be given the
> > chance to select whether to compile JPEG, GIF and XPM support, since
> > these options are selected automatically by running libgd-config.
> >
> > Lincoln
> >
> > On 11/18/06, *gang wu* <gwu at molbio.mgh.harvard.edu
> > <mailto:gwu at molbio.mgh.harvard.edu>> wrote:
> >
> >
> >     Sendu Bala wrote:
> >     > gang wu wrote:
> >     >> Hi everyone,
> >     >>
> >     >> I saw some problems when installing BioPerl
> >     >> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously
> >     CPAN could
> >     >> not solve all the dependency issues with one shot of 'install
> >     >> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be
> >     >> installed.
> >     >
> >     > What problems did you run into specifically with GD?
> >     If I enable JPEG, GIFS and  XPM,  none of the test could pass. Since
> I
> >     usually use only PNG for output, I can live without them. I am not
> >     sure
> >     if it's system related problem. All of them work fine with my 32 bit
> >     Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with
> >     newer
> >     libgd runnig Redhat AS4 AMD/EM64T does not work.
> >     >
> >     >> And it turned out that CPAN refused to install BioPerl with
> >     >> some test return value 255. Then I went to /root/.cpan/build to
> >     >> configure, test, rebuild those problematic packages. After
> >     several more
> >     >> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl
> >     >> successfully.
> >     >
> >     > Do you remember what the other problematic packages were, and
> >     what you
> >     > had to do to get them working?
> >     >
> >     XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I
> >     guess it should be XML::DOM::XPath.pm. I could not recall what other
> >     packages had issues, but basically it's special package
> >     configuration issue.
> >     >> Below attached is the output of CPAN, which stills complains
> three
> >     >> packages have issues: Data::Stag::writer HTTP::Request::Common-
> >     >> Spreadhseet::ParseExcel. I think the first two are typos
> >     somewhere in
> >     >> the Bundle::BioPerl. And the third module is not on the server
> >     and could
> >     >> be found on the CPAN site.
> >     >
> >     > All three are typos. We'll get those fixed.
> >     >
> >     >
> >     >> So my question is : Is this the right way to install BioPerl?
> >     >
> >     > At the present moment, yes. For 1.5.2 I'll probably be
> recommending
> >     > not using Bundle::BioPerl once I fix some other things.
> >     >
> >     See my another message for other issues.
> >     >
> >     >> It took me two days to figure it out but still not 100% sure all
> >     >> packages are
> >     >> installed properly.
> >     >
> >     > I'm sorry for the troubles you ran into. We'll try and do better
> for
> >     > the final release of 1.5.2.
> >     Actually your hard work is benifiting the whole community and we
> >     all owe
> >     you a Thank You.
> >
> >     _______________________________________________
> >     Bioperl-l mailing list
> >     Bioperl-l at lists.open-bio.org <mailto:Bioperl-l at lists.open-bio.org>
> >     http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> >
> > --
> > Lincoln D. Stein
> > Cold Spring Harbor Laboratory
> > 1 Bungtown Road
> > Cold Spring Harbor, NY 11724
> > (516) 367-8380 (voice)
> > (516) 367-8389 (fax)
> > FOR URGENT MESSAGES & SCHEDULING,
> > PLEASE CONTACT MY ASSISTANT,
> > SANDRA MICHELSEN, AT michelse at cshl.edu <mailto:michelse at cshl.edu>
>
>


-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse at cshl.edu


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