[Bioperl-l] Budle::BioPerl dependency issues

Sun Nov 19 03:09:08 UTC 2006

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.
>
>     _______________________________________________
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>
>
>
>
> -- 
> 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> 