[Bioperl-l] Budle::BioPerl dependency issues

gang wu gwu at molbio.mgh.harvard.edu
Mon Nov 20 13:39:55 EST 2006


No gdlib-config was found on my system. The rpm is the newest version 
from Redhat AS 4 channel for AMD/EM64T. Do you think I need to update 
the package myself? Thanks

Gang

Lincoln Stein wrote:
> 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>
>>>       
>>     
>
>
>   



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