Hi Lincoln,<div><br></div><div>Your suggested in another related thread to use the advice provided in this article: <a href="http://transfixedbutnotdead.com/2010/01/24/mac-os-x-snow-leopard-10-6-and-perl/" target="_blank">http://transfixedbutnotdead.com/2010/01/24/mac-os-x-snow-leopard-10-6-and-perl/</a></div>
<div><br></div><div>This helped me get things running after installing libgd (32-bit). Also as suggested by the article, it also helped to run:</div><div><br></div><div><span style="font-family:Georgia, 'Times New Roman', Times, serif;font-size:13px;color:rgb(51, 51, 51);line-height:22px"><i>defaults write com.apple.versioner.perl Prefer-32-Bit -bool yes</i></span></div>
<div><span style="font-family:Georgia, 'Times New Roman', Times, serif;font-size:13px;color:rgb(51, 51, 51);line-height:22px"><i>defaults write com.apple.versioner.perl Version 5.8.9</i></span></div>
<div><span style="font-family:Georgia, 'Times New Roman', Times, serif;font-size:13px;color:rgb(51, 51, 51);line-height:22px"><br></span></div><div>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.</div>
<div><br></div><div>Thanks, </div><div>Matt</div><div><br></div><div>
<div><br></div><div class="gmail_quote">On Fri, Mar 5, 2010 at 4:00 PM, Lincoln Stein <span dir="ltr"><<a href="mailto:lincoln.stein@gmail.com" target="_blank">lincoln.stein@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<div><br></div><div>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.</div><div><br></div><div>You might want to try compiling libgd2 from source.</div>
<div><br></div><div>Lincoln<div><div></div><div><br><br><div class="gmail_quote">On Wed, Mar 3, 2010 at 11:36 AM, Matthew Conte <span dir="ltr"><<a href="mailto:mconte@umd.edu" target="_blank">mconte@umd.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<div><br></div><div>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 (<a href="http://gmod.org/wiki/GBrowse_2.0_Prerequisites" target="_blank">http://gmod.org/wiki/GBrowse_2.0_Prerequisites</a>) and it seems to work (the binaries run at least). Here is the output from cpan:</div>
<div><br></div><div><div><i>cpan[6]> make GD</i></div><div><i>Running make for module 'GD'</i></div><div><i>Running make for L/LD/LDS/GD-2.44.tar.gz</i></div><div><i><br></i></div><div><i> CPAN.pm: Going to build L/LD/LDS/GD-2.44.tar.gz</i></div>
<div><i><br></i></div><div><i>Notice: Type perl Makefile.PL -h for command-line option summary.</i></div><div><i><br></i></div><div><i>Configuring for libgd version 2.0.35.</i></div><div><i>Checking for stray libgd header files...none found.</i></div>
<div><i><br></i></div><div><i>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</i></div><div><i>GD library used from: /sw</i></div>
<div><i>Checking if your kit is complete...</i></div><div><i>Looks good</i></div><div><i>Writing Makefile for GD</i></div><div><i>/usr/bin/perl GD/Image.pm.PLS GD/Image.pm</i></div><div><i>Extracting Image.pm (with variable substitutions)</i></div>
<div><i>cp GD/Polyline.pm blib/lib/GD/Polyline.pm</i></div><div><i>cp <a href="http://qd.pl" target="_blank">qd.pl</a> blib/lib/<a href="http://qd.pl" target="_blank">qd.pl</a></i></div><div><i>cp GD/Image.pm blib/lib/GD/Image.pm</i></div>
<div><i>cp GD.pm blib/lib/GD.pm</i></div>
<div><i>AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD)</i></div><div><i>cp GD/Simple.pm blib/lib/GD/Simple.pm</i></div><div><i>cp GD/Polygon.pm blib/lib/GD/Polygon.pm</i></div><div><i>cp GD/Group.pm blib/lib/GD/Group.pm</i></div>
<div><i>/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</i></div><div><i>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</i></div>
<div><i>GD.xs: In function ‘XS_GD__Image_STORABLE_thaw’:</i></div><div><i>GD.xs:923: warning: cast from pointer to integer of different size</i></div><div><i>Running Mkbootstrap for GD ()</i></div><div><i>chmod 644 GD.bs</i></div>
<div><i>rm -f blib/arch/auto/GD/GD.bundle</i></div><div><i>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 </i><span style="white-space:pre"><i> </i></span><i>\</i></div>
<div><span style="white-space:pre"><i> </i></span><i> -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 </i><span style="white-space:pre"><i> </i></span><i>\</i></div>
<div><span style="white-space:pre"><i> </i></span><i> </i></div><div><i>ld: warning: in /sw/lib/libjpeg.dylib, file is not of required architecture</i></div><div><i>ld: warning: in /sw/lib/libfreetype.dylib, file is not of required architecture</i></div>
<div><i>ld: warning: in /sw/lib/libpng12.dylib, file is not of required architecture</i></div><div><i>ld: warning: in /sw/lib/libiconv.dylib, file is not of required architecture</i></div><div><i>ld: warning: in /sw/lib/libgd.dylib, file is not of required architecture</i></div>
<div><i>ld: warning: in GD.o, file is not of required architecture</i></div><div><i>ld: warning: in GD.o, file is not of required architecture</i></div><div><i>ld: warning: in /sw/lib/libjpeg.dylib, file is not of required architecture</i></div>
<div><i>ld: warning: in /sw/lib/libfreetype.dylib, file is not of required architecture</i></div><div><i>ld: warning: in /sw/lib/libpng12.dylib, file is not of required architecture</i></div><div><i>ld: warning: in /sw/lib/libiconv.dylib, file is not of required architecture</i></div>
<div><i>ld: warning: in /sw/lib/libgd.dylib, file is not of required architecture</i></div><div><i>chmod 755 blib/arch/auto/GD/GD.bundle</i></div><div><i>cp GD.bs blib/arch/auto/GD/GD.bs</i></div><div><i>chmod 644 blib/arch/auto/GD/GD.bs</i></div>
<div><i>/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bdf_scripts/bdf2gdfont.PLS bdf_scripts/<a href="http://bdf2gdfont.pl" target="_blank">bdf2gdfont.pl</a></i></div><div><i>Extracting <a href="http://bdf2gdfont.pl" target="_blank">bdf2gdfont.pl</a> (with variable substitutions)</i></div>
<div><i>cp bdf_scripts/<a href="http://bdf2gdfont.pl" target="_blank">bdf2gdfont.pl</a> blib/script/<a href="http://bdf2gdfont.pl" target="_blank">bdf2gdfont.pl</a></i></div><div><i>/usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/<a href="http://bdf2gdfont.pl" target="_blank">bdf2gdfont.pl</a></i></div>
<div><i>Manifying blib/man1/bdf2gdfont.pl.1</i></div><div><i>Manifying blib/man3/GD::Polyline.3pm</i></div><div><i>Manifying blib/man3/GD::Image.3pm</i></div><div><i>Manifying blib/man3/GD::Simple.3pm</i></div><div><i>Manifying blib/man3/GD.3pm</i></div>
<div><i>Manifying blib/man3/GD::Polygon.3pm</i></div><div><i> LDS/GD-2.44.tar.gz</i></div><div><i> /usr/bin/make -- OK</i></div><div><i>Warning (usually harmless): 'YAML' not installed, will not store persistent state</i></div>
<div><i><br></i></div><div><i>cpan[7]> test GD</i></div><div><i>Running test for module 'GD'</i></div><div><i>Running make for L/LD/LDS/GD-2.44.tar.gz</i></div><div><i> Has already been unwrapped into directory /Users/matt/.cpan/build/GD-2.44-rscDlg</i></div>
<div><i> Has already been made</i></div><div><i>Running make test</i></div><div><i>PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t</i></div>
<div><i>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</i></div><div><i> Referenced from: /Users/matt/.cpan/build/GD-2.44-rscDlg/blib/arch/auto/GD/GD.bundle</i></div>
<div><i> Expected in: flat namespace</i></div><div><i> 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.</i></div>
<div><i> at t/GD.t line 14</i></div><div><i>Compilation failed in require at t/GD.t line 14.</i></div><div><i>BEGIN failed--compilation aborted at t/GD.t line 14.</i></div><div><i>t/GD..........dubious </i></div>
<div><span style="white-space:pre"><i> </i></span><i>Test returned status 2 (wstat 512, 0x200)</i></div><div><i>DIED. FAILED tests 1-12</i></div><div><span style="white-space:pre"><i> </i></span><i>Failed 12/12 tests, 0.00% okay</i></div>
<div><i>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</i></div>
<div><i> Referenced from: /Users/matt/.cpan/build/GD-2.44-rscDlg/blib/arch/auto/GD/GD.bundle</i></div><div><i> Expected in: flat namespace</i></div><div><i> 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.</i></div>
<div><i> at /Users/matt/.cpan/build/GD-2.44-rscDlg/blib/lib/GD/Polyline.pm line 45</i></div><div><i>Compilation failed in require at /Users/matt/.cpan/build/GD-2.44-rscDlg/blib/lib/GD/Polyline.pm line 45.</i></div>
<div><i>BEGIN failed--compilation aborted at /Users/matt/.cpan/build/GD-2.44-rscDlg/blib/lib/GD/Polyline.pm line 45.</i></div><div><i>Compilation failed in require at t/Polyline.t line 10.</i></div><div><i>BEGIN failed--compilation aborted at t/Polyline.t line 10.</i></div>
<div><i>t/Polyline....dubious </i></div><div><span style="white-space:pre"><i> </i></span><i>Test returned status 2 (wstat 512, 0x200)</i></div>
<div><i>DIED. FAILED test 1</i></div><div><span style="white-space:pre"><i> </i></span><i>Failed 1/1 tests, 0.00% okay</i></div><div><i>Failed Test Stat Wstat Total Fail List of Failed</i></div><div>
<i>-------------------------------------------------------------------------------</i></div><div><i>t/GD.t 2 512 12 23 1-12</i></div><div><i>t/Polyline.t 2 512 1 2 1</i></div><div><i>Failed 2/2 test scripts. 13/13 subtests failed.</i></div>
<div><i>Files=2, Tests=13, 0 wallclock secs ( 0.05 cusr + 0.01 csys = 0.06 CPU)</i></div><div><i>Failed 2/2 test programs. 13/13 subtests failed.</i></div><div><i>make: *** [test_dynamic] Error 2</i></div><div><i> LDS/GD-2.44.tar.gz</i></div>
<div><i> /usr/bin/make test -- NOT OK</i></div><div><i>//hint// to see the cpan-testers results for installing this module, try:</i></div><div><i> reports LDS/GD-2.44.tar.gz</i></div><div><i>Warning (usually harmless): 'YAML' not installed, will not store persistent state</i></div>
<div><i>Failed during this command:</i></div><div><i> LDS/GD-2.44.tar.gz : make_test NO</i></div><div><i><br></i></div><div><i><br></i></div><div><i><br></i></div><div>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:</div>
<div><br></div><div><br></div><div><br></div><div><div><i>dev:GD-2.44 matt$ perl Makefile.PL</i></div><div><i>Notice: Type perl Makefile.PL -h for command-line option summary.</i></div><div><i><br></i></div><div><i>Configuring for libgd version 2.0.35.</i></div>
<div><i>Checking for stray libgd header files...none found.</i></div><div><i><br></i></div><div><i>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</i></div>
<div><i>GD library used from: /usr/local/genome</i></div><div><i>Checking if your kit is complete...</i></div><div><i>Looks good</i></div><div><i>Writing Makefile for GD</i></div><div><i>dev:GD-2.44 matt$ make</i></div>
<div><i>/usr/bin/perl GD/Image.pm.PLS GD/Image.pm</i></div><div><i>Extracting Image.pm (with variable substitutions)</i></div><div><i>cp GD/Polyline.pm blib/lib/GD/Polyline.pm</i></div><div><i>cp <a href="http://qd.pl" target="_blank">qd.pl</a> blib/lib/<a href="http://qd.pl" target="_blank">qd.pl</a></i></div>
<div><i>cp GD/Image.pm blib/lib/GD/Image.pm</i></div><div><i>cp GD.pm blib/lib/GD.pm</i></div><div><i>AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD)</i></div><div><i>cp GD/Simple.pm blib/lib/GD/Simple.pm</i></div><div><i>cp GD/Polygon.pm blib/lib/GD/Polygon.pm</i></div>
<div><i>cp GD/Group.pm blib/lib/GD/Group.pm</i></div><div><i>/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</i></div>
<div><i>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</i></div>
<div><i>GD.xs: In function ‘XS_GD__Image_STORABLE_thaw’:</i></div><div><i>GD.xs:923: warning: cast from pointer to integer of different size</i></div><div><i>Running Mkbootstrap for GD ()</i></div><div><i>chmod 644 GD.bs</i></div>
<div><i>rm -f blib/arch/auto/GD/GD.bundle</i></div><div><i>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 </i><span style="white-space:pre"><i> </i></span><i>\</i></div>
<div><span style="white-space:pre"><i> </i></span><i> -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 </i><span style="white-space:pre"><i> </i></span><i>\</i></div>
<div><span style="white-space:pre"><i> </i></span><i> </i></div><div><i>ld: warning: in GD.o, file is not of required architecture</i></div><div><i>ld: warning: in /usr/local/genome/lib/libjpeg.dylib, file is not of required architecture</i></div>
<div><i>ld: warning: in /usr/local/genome/lib/libfreetype.dylib, file is not of required architecture</i></div><div><i>ld: warning: in /usr/local/genome/lib/libgd.dylib, file is not of required architecture</i></div><div>
<i>ld: warning: in GD.o, file is not of required architecture</i></div><div><i>ld: warning: in /usr/local/genome/lib/libjpeg.dylib, file is not of required architecture</i></div><div><i>ld: warning: in /usr/local/genome/lib/libfreetype.dylib, file is not of required architecture</i></div>
<div><i>ld: warning: in /usr/local/genome/lib/libgd.dylib, file is not of required architecture</i></div><div><i>chmod 755 blib/arch/auto/GD/GD.bundle</i></div><div><i>cp GD.bs blib/arch/auto/GD/GD.bs</i></div><div><i>chmod 644 blib/arch/auto/GD/GD.bs</i></div>
<div><i>/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bdf_scripts/bdf2gdfont.PLS bdf_scripts/<a href="http://bdf2gdfont.pl" target="_blank">bdf2gdfont.pl</a></i></div><div><i>Extracting <a href="http://bdf2gdfont.pl" target="_blank">bdf2gdfont.pl</a> (with variable substitutions)</i></div>
<div><i>cp bdf_scripts/<a href="http://bdf2gdfont.pl" target="_blank">bdf2gdfont.pl</a> blib/script/<a href="http://bdf2gdfont.pl" target="_blank">bdf2gdfont.pl</a></i></div><div><i>/usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/<a href="http://bdf2gdfont.pl" target="_blank">bdf2gdfont.pl</a></i></div>
<div><i>Manifying blib/man1/bdf2gdfont.pl.1</i></div><div><i>Manifying blib/man3/GD::Polyline.3pm</i></div><div><i>Manifying blib/man3/GD::Image.3pm</i></div><div><i>Manifying blib/man3/GD::Simple.3pm</i></div><div><i>Manifying blib/man3/GD.3pm</i></div>
<div><i>Manifying blib/man3/GD::Polygon.3pm</i></div><div><i>dev:GD-2.44 matt$ make test</i></div><div><i>PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t</i></div>
<div><i>t/GD..........Can't find 'boot_GD' symbol in ./blib/arch/auto/GD/GD.bundle</i></div><div><i> at t/GD.t line 14</i></div><div><i>Compilation failed in require at t/GD.t line 14.</i></div><div><i>BEGIN failed--compilation aborted at t/GD.t line 14.</i></div>
<div><i>t/GD..........dubious </i></div><div><span style="white-space:pre"><i> </i></span><i>Test returned status 2 (wstat 512, 0x200)</i></div>
<div><i>DIED. FAILED tests 1-12</i></div><div><span style="white-space:pre"><i> </i></span><i>Failed 12/12 tests, 0.00% okay</i></div><div><i>t/Polyline....Can't find 'boot_GD' symbol in /Users/matt/Desktop/Matt/software/GD-2.44/blib/arch/auto/GD/GD.bundle</i></div>
<div><i> at /Users/matt/Desktop/Matt/software/GD-2.44/blib/lib/GD/Polyline.pm line 45</i></div><div><i>Compilation failed in require at /Users/matt/Desktop/Matt/software/GD-2.44/blib/lib/GD/Polyline.pm line 45.</i></div>
<div>
<i>BEGIN failed--compilation aborted at /Users/matt/Desktop/Matt/software/GD-2.44/blib/lib/GD/Polyline.pm line 45.</i></div><div><i>Compilation failed in require at t/Polyline.t line 10.</i></div><div><i>BEGIN failed--compilation aborted at t/Polyline.t line 10.</i></div>
<div><i>t/Polyline....dubious </i></div><div><span style="white-space:pre"><i> </i></span><i>Test returned status 2 (wstat 512, 0x200)</i></div>
<div><i>DIED. FAILED test 1</i></div><div><span style="white-space:pre"><i> </i></span><i>Failed 1/1 tests, 0.00% okay</i></div><div><i>Failed Test Stat Wstat Total Fail List of Failed</i></div><div>
<i>-------------------------------------------------------------------------------</i></div><div><i>t/GD.t 2 512 12 23 1-12</i></div><div><i>t/Polyline.t 2 512 1 2 1</i></div><div><i>Failed 2/2 test scripts. 13/13 subtests failed.</i></div>
<div><i>Files=2, Tests=13, 0 wallclock secs ( 0.05 cusr + 0.01 csys = 0.06 CPU)</i></div><div><i>Failed 2/2 test programs. 13/13 subtests failed.</i></div><div><i>make: *** [test_dynamic] Error 2</i></div><div><br></div>
<div><br></div></div><div><br></div><div>I can get rid of the ld "<i>file is not of required architecture" </i>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?</div>
<div><br></div><div>Thanks,<br>Matt</div></div>
</blockquote></div><br><br clear="all"><br></div></div>-- <br>Lincoln D. Stein<br>Director, Informatics and Biocomputing Platform<br>Ontario Institute for Cancer Research<br>101 College St., Suite 800<br>Toronto, ON, Canada M5G0A3<br>
416 673-8514<br>Assistant: Renata Musa <<a href="mailto:Renata.Musa@oicr.on.ca" target="_blank">Renata.Musa@oicr.on.ca</a>><br>
</div>
</blockquote></div><br></div>