[Gmod-help] GBrowse 2.0 install on mac OSX 10.6 server
Matthew Conte
mconte at umd.edu
Wed Mar 10 13:03:07 EST 2010
Hi Lincoln,
Your suggested in another related thread to use the advice provided in this
article:
http://transfixedbutnotdead.com/2010/01/24/mac-os-x-snow-leopard-10-6-and-perl/
This helped me get things running after installing libgd (32-bit). Also as
suggested by the article, it also helped to run:
*defaults write com.apple.versioner.perl Prefer-32-Bit -bool yes*
*defaults write com.apple.versioner.perl Version 5.8.9*
as both my regular user and with sudo to get CPAN to install the perl GD and
other modules in the perl 5.8.9 library and not the 5.10.0 library.
Thanks,
Matt
On Fri, Mar 5, 2010 at 4:00 PM, Lincoln Stein <lincoln.stein at gmail.com>wrote:
> 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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