[Gmod-help] GBrowse 2.0 install on mac OSX 10.6 server
Matthew Conte
mconte at umd.edu
Wed Mar 3 11:36:29 EST 2010
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
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