[Gmod-help] GBrowse 2.0 install on mac OSX 10.6 server
Lincoln Stein
lincoln.stein at gmail.com
Fri Mar 5 16:00:19 EST 2010
Hi,
If your perl is 64-bit, then you need to install the 64-bit version of the
gd2 library. I think you are installing the 32-bit version.
You might want to try compiling libgd2 from source.
Lincoln
On Wed, Mar 3, 2010 at 11:36 AM, Matthew Conte <mconte at umd.edu> wrote:
> Hi all,
>
> I'm trying to get GBrowse 2.0 installed on OSX 10.6.2 server (64bit). I
> can't seem to get the GD perl module to get past the 'make test' step
> though. I've installed gd2/gd2-bin via fink as suggested (
> http://gmod.org/wiki/GBrowse_2.0_Prerequisites) and it seems to work (the
> binaries run at least). Here is the output from cpan:
>
> *cpan[6]> make GD*
> *Running make for module 'GD'*
> *Running make for L/LD/LDS/GD-2.44.tar.gz*
> *
> *
> * CPAN.pm: Going to build L/LD/LDS/GD-2.44.tar.gz*
> *
> *
> *Notice: Type perl Makefile.PL -h for command-line option summary.*
> *
> *
> *Configuring for libgd version 2.0.35.*
> *Checking for stray libgd header files...none found.*
> *
> *
> *Included Features: GD_XPM GD_JPEG GD_FONTCONFIG GD_FREETYPE
> GD_PNG GD_GIF GD_GIFANIM GD_OPENPOLYGON GD_UNCLOSEDPOLY GD_ANIMGIF
> GD_FTCIRCLE VERSION_33*
> *GD library used from: /sw*
> *Checking if your kit is complete...*
> *Looks good*
> *Writing Makefile for GD*
> */usr/bin/perl GD/Image.pm.PLS GD/Image.pm*
> *Extracting Image.pm (with variable substitutions)*
> *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*
> *cp GD/Group.pm blib/lib/GD/Group.pm*
> */usr/bin/perl /System/Library/Perl/5.10.0/ExtUtils/xsubpp -typemap
> /System/Library/Perl/5.10.0/ExtUtils/typemap -typemap typemap GD.xs >
> GD.xsc && mv GD.xsc GD.c*
> *gcc-4.2 -c -I/sw/include -Wformat=0 -Os -DVERSION=\"2.44\"
> -DXS_VERSION=\"2.44\"
> "-I/System/Library/Perl/5.10.0/darwin-thread-multi-2level/CORE"
> -DHAVE_JPEG -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF
> -DVERSION_33 -DHAVE_UNCLOSEDPOLY -DHAVE_FONTCONFIG -DHAVE_FTCIRCLE GD.c*
> *GD.xs: In function ‘XS_GD__Image_STORABLE_thaw’:*
> *GD.xs:923: warning: cast from pointer to integer of different size*
> *Running Mkbootstrap for GD ()*
> *chmod 644 GD.bs*
> *rm -f blib/arch/auto/GD/GD.bundle*
> *LD_RUN_PATH="/usr/X11R6/lib:/sw/lib:/sw/lib/fontconfig2/lib:/usr/lib"
> gcc-4.2 -mmacosx-version-min=10.6 -arch x86_64 -arch i386 -arch ppc -bundle
> -undefined dynamic_lookup -L/usr/local/lib GD.o -o
> blib/arch/auto/GD/GD.bundle ** **\*
> * ** -L/sw/lib -L/sw/lib -L/sw/lib/fontconfig2/lib -L/sw/lib
> -L/usr/X11R6/lib -L/sw/lib/fontconfig2/lib -L/sw/lib -lXpm -lX11 -ljpeg
> -lfontconfig -lfreetype -lpng12 -lz -liconv -lgd ** **\*
> * ** *
> *ld: warning: in /sw/lib/libjpeg.dylib, file is not of required
> architecture*
> *ld: warning: in /sw/lib/libfreetype.dylib, file is not of required
> architecture*
> *ld: warning: in /sw/lib/libpng12.dylib, file is not of required
> architecture*
> *ld: warning: in /sw/lib/libiconv.dylib, file is not of required
> architecture*
> *ld: warning: in /sw/lib/libgd.dylib, file is not of required architecture
> *
> *ld: warning: in GD.o, file is not of required architecture*
> *ld: warning: in GD.o, file is not of required architecture*
> *ld: warning: in /sw/lib/libjpeg.dylib, file is not of required
> architecture*
> *ld: warning: in /sw/lib/libfreetype.dylib, file is not of required
> architecture*
> *ld: warning: in /sw/lib/libpng12.dylib, file is not of required
> architecture*
> *ld: warning: in /sw/lib/libiconv.dylib, file is not of required
> architecture*
> *ld: warning: in /sw/lib/libgd.dylib, file is not of required architecture
> *
> *chmod 755 blib/arch/auto/GD/GD.bundle*
> *cp GD.bs blib/arch/auto/GD/GD.bs*
> *chmod 644 blib/arch/auto/GD/GD.bs*
> */usr/bin/perl "-Iblib/arch" "-Iblib/lib" bdf_scripts/bdf2gdfont.PLS
> bdf_scripts/bdf2gdfont.pl*
> *Extracting bdf2gdfont.pl (with variable substitutions)*
> *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*
> * LDS/GD-2.44.tar.gz*
> * /usr/bin/make -- OK*
> *Warning (usually harmless): 'YAML' not installed, will not store
> persistent state*
> *
> *
> *cpan[7]> test GD*
> *Running test for module 'GD'*
> *Running make for L/LD/LDS/GD-2.44.tar.gz*
> * Has already been unwrapped into directory
> /Users/matt/.cpan/build/GD-2.44-rscDlg*
> * Has already been made*
> *Running 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.bundle' for module GD:
> dlopen(./blib/arch/auto/GD/GD.bundle, 2): Symbol not found:
> _gdFTUseFontConfig*
> * Referenced from:
> /Users/matt/.cpan/build/GD-2.44-rscDlg/blib/arch/auto/GD/GD.bundle*
> * Expected in: flat namespace*
> * in /Users/matt/.cpan/build/GD-2.44-rscDlg/blib/arch/auto/GD/GD.bundle at
> /System/Library/Perl/5.10.0/darwin-thread-multi-2level/DynaLoader.pm line
> 207.*
> * 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 2 (wstat 512, 0x200)*
> *DIED. FAILED tests 1-12*
> * **Failed 12/12 tests, 0.00% okay*
> *t/Polyline....Can't load
> '/Users/matt/.cpan/build/GD-2.44-rscDlg/blib/arch/auto/GD/GD.bundle' for
> module GD:
> dlopen(/Users/matt/.cpan/build/GD-2.44-rscDlg/blib/arch/auto/GD/GD.bundle,
> 2): Symbol not found: _gdFTUseFontConfig*
> * Referenced from:
> /Users/matt/.cpan/build/GD-2.44-rscDlg/blib/arch/auto/GD/GD.bundle*
> * Expected in: flat namespace*
> * in /Users/matt/.cpan/build/GD-2.44-rscDlg/blib/arch/auto/GD/GD.bundle at
> /System/Library/Perl/5.10.0/darwin-thread-multi-2level/DynaLoader.pm line
> 207.*
> * at /Users/matt/.cpan/build/GD-2.44-rscDlg/blib/lib/GD/Polyline.pm line
> 45*
> *Compilation failed in require at
> /Users/matt/.cpan/build/GD-2.44-rscDlg/blib/lib/GD/Polyline.pm line 45.*
> *BEGIN failed--compilation aborted at
> /Users/matt/.cpan/build/GD-2.44-rscDlg/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 2 (wstat 512, 0x200)*
> *DIED. FAILED test 1*
> * **Failed 1/1 tests, 0.00% okay*
> *Failed Test Stat Wstat Total Fail List of Failed*
> *
> -------------------------------------------------------------------------------
> *
> *t/GD.t 2 512 12 23 1-12*
> *t/Polyline.t 2 512 1 2 1*
> *Failed 2/2 test scripts. 13/13 subtests failed.*
> *Files=2, Tests=13, 0 wallclock secs ( 0.05 cusr + 0.01 csys = 0.06
> CPU)*
> *Failed 2/2 test programs. 13/13 subtests failed.*
> *make: *** [test_dynamic] Error 2*
> * LDS/GD-2.44.tar.gz*
> * /usr/bin/make test -- NOT OK*
> *//hint// to see the cpan-testers results for installing this module, try:
> *
> * reports LDS/GD-2.44.tar.gz*
> *Warning (usually harmless): 'YAML' not installed, will not store
> persistent state*
> *Failed during this command:*
> * LDS/GD-2.44.tar.gz : make_test NO*
> *
> *
> *
> *
> *
> *
> I've also installed gd and its dependencies manually to make sure it built
> correctly and I get a similar error when installing GD-2.44 manually:
>
>
>
> *dev:GD-2.44 matt$ perl Makefile.PL*
> *Notice: Type perl Makefile.PL -h for command-line option summary.*
> *
> *
> *Configuring for libgd version 2.0.35.*
> *Checking for stray libgd header files...none found.*
> *
> *
> *Included Features: GD_XPM GD_JPEG GD_FONTCONFIG GD_FREETYPE
> GD_PNG GD_GIF GD_GIFANIM GD_OPENPOLYGON GD_UNCLOSEDPOLY GD_ANIMGIF
> GD_FTCIRCLE VERSION_33*
> *GD library used from: /usr/local/genome*
> *Checking if your kit is complete...*
> *Looks good*
> *Writing Makefile for GD*
> *dev:GD-2.44 matt$ make*
> */usr/bin/perl GD/Image.pm.PLS GD/Image.pm*
> *Extracting Image.pm (with variable substitutions)*
> *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*
> *cp GD/Group.pm blib/lib/GD/Group.pm*
> */usr/bin/perl /System/Library/Perl/5.10.0/ExtUtils/xsubpp -typemap
> /System/Library/Perl/5.10.0/ExtUtils/typemap -typemap typemap GD.xs >
> GD.xsc && mv GD.xsc GD.c*
> *gcc-4.2 -c -I/usr/local/genome/include -Wformat=0 -Os
> -DVERSION=\"2.44\" -DXS_VERSION=\"2.44\"
> "-I/System/Library/Perl/5.10.0/darwin-thread-multi-2level/CORE"
> -DHAVE_JPEG -DHAVE_FT -DHAVE_XPM -DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF
> -DVERSION_33 -DHAVE_UNCLOSEDPOLY -DHAVE_FONTCONFIG -DHAVE_FTCIRCLE GD.c*
> *GD.xs: In function ‘XS_GD__Image_STORABLE_thaw’:*
> *GD.xs:923: warning: cast from pointer to integer of different size*
> *Running Mkbootstrap for GD ()*
> *chmod 644 GD.bs*
> *rm -f blib/arch/auto/GD/GD.bundle*
> *LD_RUN_PATH="/usr/X11/lib:/usr/local/genome/lib:/usr/lib" gcc-4.2
> -mmacosx-version-min=10.6 -arch x86_64 -arch i386 -arch ppc -bundle
> -undefined dynamic_lookup -L/usr/local/lib GD.o -o
> blib/arch/auto/GD/GD.bundle ** **\*
> * ** -L/usr/local/genome/lib -L/usr/X11/lib -L/usr/X11R6/lib/
> -L/usr/local/genome//lib -L/usr/local/genome/lib -lXpm -lX11 -ljpeg
> -lfontconfig -lfreetype -lpng12 -lz -liconv -lgd ** **\*
> * ** *
> *ld: warning: in GD.o, file is not of required architecture*
> *ld: warning: in /usr/local/genome/lib/libjpeg.dylib, file is not of
> required architecture*
> *ld: warning: in /usr/local/genome/lib/libfreetype.dylib, file is not of
> required architecture*
> *ld: warning: in /usr/local/genome/lib/libgd.dylib, file is not of
> required architecture*
> *ld: warning: in GD.o, file is not of required architecture*
> *ld: warning: in /usr/local/genome/lib/libjpeg.dylib, file is not of
> required architecture*
> *ld: warning: in /usr/local/genome/lib/libfreetype.dylib, file is not of
> required architecture*
> *ld: warning: in /usr/local/genome/lib/libgd.dylib, file is not of
> required architecture*
> *chmod 755 blib/arch/auto/GD/GD.bundle*
> *cp GD.bs blib/arch/auto/GD/GD.bs*
> *chmod 644 blib/arch/auto/GD/GD.bs*
> */usr/bin/perl "-Iblib/arch" "-Iblib/lib" bdf_scripts/bdf2gdfont.PLS
> bdf_scripts/bdf2gdfont.pl*
> *Extracting bdf2gdfont.pl (with variable substitutions)*
> *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*
> *dev:GD-2.44 matt$ 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 find 'boot_GD' symbol in
> ./blib/arch/auto/GD/GD.bundle*
> * 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 2 (wstat 512, 0x200)*
> *DIED. FAILED tests 1-12*
> * **Failed 12/12 tests, 0.00% okay*
> *t/Polyline....Can't find 'boot_GD' symbol in
> /Users/matt/Desktop/Matt/software/GD-2.44/blib/arch/auto/GD/GD.bundle*
> * at /Users/matt/Desktop/Matt/software/GD-2.44/blib/lib/GD/Polyline.pm
> line 45*
> *Compilation failed in require at
> /Users/matt/Desktop/Matt/software/GD-2.44/blib/lib/GD/Polyline.pm line 45.
> *
> *BEGIN failed--compilation aborted at
> /Users/matt/Desktop/Matt/software/GD-2.44/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 2 (wstat 512, 0x200)*
> *DIED. FAILED test 1*
> * **Failed 1/1 tests, 0.00% okay*
> *Failed Test Stat Wstat Total Fail List of Failed*
> *
> -------------------------------------------------------------------------------
> *
> *t/GD.t 2 512 12 23 1-12*
> *t/Polyline.t 2 512 1 2 1*
> *Failed 2/2 test scripts. 13/13 subtests failed.*
> *Files=2, Tests=13, 0 wallclock secs ( 0.05 cusr + 0.01 csys = 0.06
> CPU)*
> *Failed 2/2 test programs. 13/13 subtests failed.*
> *make: *** [test_dynamic] Error 2*
>
>
>
> I can get rid of the ld "*file is not of required architecture" *warnings
> during make if I remove -arch ppc and -arch i386 from the make file, but
> make test still fails. Anyone run into this before or have any suggestions?
>
> Thanks,
> Matt
>
--
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 at oicr.on.ca>
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