TTf support for Mac

[Himanshu Sharma]

Hi Martin,

I have Compiled GD lib and I can see freetype gd when I try both. I am using Circos-0.64 . Here is my output of the commands you suggest and error that I am getting. I am using Mac as well.

perl Makefile.PL 

Notice: Type perl Makefile.PL -h for command-line option summary.

Configuring for libgd version 2.1.0.

Checking for stray libgd header files...none found.

Included Features:          GD_JPEG GD_FREETYPE GD_PNG GD_GIF GD_GIFANIM GD_OPENPOLYGON

GD library used from:       /usr/local

Checking if your kit is complete...

Looks good

Writing Makefile for GD

gdlib-config --all

GD library  2.1.0

includedir: /usr/local/include

cflags:     -I/usr/local/include

ldflags:     -L/usr/X11/lib -L/usr/local/lib

libs:       -ljpeg -lz  -L/usr/local/lib -lpng16 -L/usr/local/lib -lfreetype -lz -lbz2 -liconv

libdir:     /usr/local/lib

features:   GD_JPEG GD_FREETYPE GD_PNG GD_GIF GD_GIFANIM GD_OPENPOLYGON

Error : *** CIRCOS ERROR ***

  There was a problem with True Type font support. Circos could not render text

  from the font file

      /Users/hsharma/Documents/circos-0.64/fonts/symbols/symbols.otf

  Please check that gd (system graphics library) and GD (Perl's interface to gd)

  are compiled with True Type support.

  On UNIX systems, try

      gdlib-config --all

  and look for GD_FREETYPE in the 'features' line and -lfreetype in the 'libs'

  line. If these are there, it's likely that your Perl GD module needs

  recompiling.

  For help in installing libgd and/or GD, see

      http://www.perlmonks.org/?node_id=621579

  If you are having trouble debugging this error, use this tutorial to learn how

  to use the debugging facility

      http://www.circos.ca/tutorials/lessons/configuration/debugging

  If you're still stumped, get support in the Circos Google Group

      http://groups.google.com/group/circos-data-visualization

  Stack trace:

 at /Users/hsharma/Documents/circos-0.64/bin/../lib/Circos/Error.pm line 354

Circos::Error::fatal_error('font', 'no_ttf', '/Users/hsharma/Documents/circos-0.64/fonts/symbols/symbols.otf') called at /Users/hsharma/Documents/circos-0.64/bin/../lib/Circos/Font.pm line 192

Circos::Font::get_label_size('font_file', '/Users/hsharma/Documents/circos-0.64/fonts/symbols/symbols.otf', 'size', 10, 'text', 'abc123') called at /Users/hsharma/Documents/circos-0.64/bin/../lib/Circos/Font.pm line 243

Circos::Font::sanity_check() called at /Users/hsharma/Documents/circos-0.64/bin/../lib/Circos.pm line 771

Circos::run('Circos', 'configfile', '../plots/resistant.conf') called at ./bin/circos line 300

Can you suggest me what I should try next ?.

Thanks,

Himanshu

[Martin Krzywinski]

Based on this error

Circos::Font::get_label_size('font_file', '/Users/hsharma/Documents/circos-0.64/fonts/symbols/symbols.otf', 'size', 10, 'text', 'abc123') called at /Users/hsharma/Documents/circos-0.64/bin/../lib/Circos/Font.pm line 243

it looks like you're trying to use the symbols font to render the text "abc123". This font is special and doesn't define all characters.

Can you run bin/gddiag to create this test image

http://www.circos.ca/documentation/tutorials/configuration/png_output/images

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Samantha]

Hi Martin,

I'm sure you're sick of GD issues at this point, but like so many before me I'm super new to all of this and don't really know what to do.
I think I'm encountering a nearly identical problem to the one on this feed.
Things start fine, then I get:

*** CIRCOS ERROR ***

  There was a problem with True Type font support. Circos could not render text
  from the font file

      /Applications/circos100813/bin/../fonts/symbols/symbols.otf

etc...

 Stack trace:
 at /Applications/circos100813/bin/../lib/Circos/Error.pm line 354
    Circos::Error::fatal_error('font', 'no_ttf', '/Applications/circos100813/bin/../fonts/symbols/symbols.otf') called at /Applications/circos100813/bin/../lib/Circos/Font.pm line 192
    Circos::Font::get_label_size('font_file', '/Applications/circos100813/bin/../fonts/symbols/symbols.otf', 'size', 10, 'text', 'abc123') called at /Applications/circos100813/bin/../lib/Circos/Font.pm line 243
    Circos::Font::sanity_check() called at /Applications/circos100813/bin/../lib/Circos.pm line 771
    Circos::run('Circos', 'configfile', '/Applications/circos100813/etc/eremophORPIariz.ashx/circos/ci...') called at ./circos line 300

- So as you suggested up here I tried "bin/gddiag" and saw this error

$ perl ./gddiag  /Applications/circos100813/etc/eremophORPIariz.ashx/circos/circos.conf
allocated 29202 colors
Can't locate object method "png" via package "GD::Image" at ./gddiag line 209.

So there is something wrong with my GD:Image module?

when I run ./test.modules it says "ok" next to everything.
also when I run gdlib-config --all
I see this:

GD library  2.0.33
includedir: /usr/local/include
cflags:     -I/usr/local/include
ldflags:     -L/usr/X11/lib -Wl,-framework,CoreServices -Wl,-framework,ApplicationServices  -L/usr/X11/lib
libs:       -lXpm -lX11 -lfontconfig -lfreetype -lpng12 -lz  -liconv
libdir:     /usr/local/lib
features:   GD_XPM GD_FONTCONFIG GD_FREETYPE GD_PNG GD_GIF

Which is supposed to be good news right? Since freetype is listed where it needs to be?

Got any tips of where I should go from here?
I hadn't typed a word of code until ~2weeks ago, so go easy on me :) 
Thanks so much
-Sam

[Martin Krzywinski]

The test.modules script only verifies that the modules are installed. In some cases, a module could be installed but still malfunctioning, if it wasn't hooked into the system libraries correctly.

To run gddiag, you don't need "perl gddiag"

$ bin/gddiag

is enough. The perl interpreter will automatically be called to parse the script. 

> Can't locate object method "png" via package "GD::Image" at ./gddiag line 209.

This error suggests that the GD perl module is not correctly installed. It looks like you have libgd, and it has the right features. During the installation of the GD module, the build script looks for libgd - this step may have barfed. 

You should try installing GD manually. Get the source from 

http://search.cpan.org/CPAN/authors/id/L/LD/LDS/GD-2.50.tar.gz

Once unpacked, here's what installation looks like on my Mac (10.6.8)

$ 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

Checking if your kit is complete...

Looks good

Writing Makefile for GD

Then run

$ make

$ make test

$ make install

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

[Samantha]

That worked!
I had been seeing "Makefile.PL" in these feeds and didn't know where it was coming from

Thanks so so very much!

[Brendan Kohrn]

Martin, 

I'm having a similar error, only when I try to install GD manually, I get this:

>: perl Makefile.PL

Notice: Type perl Makefile.PL -h for command-line option summary.

Configuring for libgd version 2.1.0.

Checking for stray libgd header files...none found.

Included Features:          GD_GIF GD_GIFANIM GD_OPENPOLYGON

GD library used from:       /usr/local

Generating a Unix-style Makefile

Writing Makefile for GD

Writing MYMETA.yml and MYMETA.json

>: 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/Simple.pm blib/lib/GD/Simple.pm

cp GD.pm blib/lib/GD.pm

AutoSplitting blib/lib/GD.pm (blib/lib/auto/GD)

cp GD/Polygon.pm blib/lib/GD/Polygon.pm

cp GD/Group.pm blib/lib/GD/Group.pm

Running Mkbootstrap for GD ()

chmod 644 GD.bs

/usr/bin/perl /Library/Perl/5.12/ExtUtils/xsubpp  -typemap /System/Library/Perl/5.12/ExtUtils/typemap -typemap typemap  GD.xs > GD.xsc && mv GD.xsc GD.c

llvm-gcc-4.2 -c  -I/usr/local/include -arch x86_64 -arch i386 -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -fstack-protector -I/usr/local/include -Wformat=0 -Os   -DVERSION=\"2.52\" -DXS_VERSION=\"2.52\"  "-I/System/Library/Perl/5.12/darwin-thread-multi-2level/CORE"  -DHAVE_GIF GD.c

rm -f blib/arch/auto/GD/GD.bundle

LD_RUN_PATH="/usr/lib:/usr/local/lib" llvm-gcc-4.2 -mmacosx-version-min=10.7  -arch x86_64 -arch i386 -bundle -undefined dynamic_lookup -L/usr/local/lib -fstack-protector GD.o  -o blib/arch/auto/GD/GD.bundle \

  -L/usr/X11/lib -L/usr/local/lib -lz -liconv -lgd   \

 

ld: warning: ignoring file /usr/local/lib/libgd.dylib, file was built for unsupported file format which is not the architecture being linked (i386)

chmod 755 blib/arch/auto/GD/GD.bundle

/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- GD.bs blib/arch/auto/GD/GD.bs 644

/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.3pm

Manifying blib/man3/GD::Image.3pm

Manifying blib/man3/GD::Polygon.3pm

Manifying blib/man3/GD::Polyline.3pm

Manifying blib/man3/GD::Simple.3pm

>: make test

Running Mkbootstrap for GD ()

chmod 644 GD.bs

PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t

t/GD.t ........ 1/12 Testing using gif support.

t/GD.t ........ Failed 6/12 subtests 

(less 3 skipped subtests: 3 okay)

t/Polyline.t .. ok   

Test Summary Report

-------------------

t/GD.t      (Wstat: 0 Tests: 12 Failed: 6)

  Failed tests:  2-7

Files=2, Tests=13,  0 wallclock secs ( 0.02 usr  0.01 sys +  0.09 cusr  0.01 csys =  0.13 CPU)

Result: FAIL

Failed 1/2 test programs. 6/13 subtests failed.

make: *** [test_dynamic] Error 255

Any advice?  

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[Martin Krzywinski]

You're missing FreeType support in libgd. The features line should have GD_FREETYPE.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Junhao Wen]

It's really frustrating. 

I got the same error, and then I installed FreeType:

sudo cpanm Font::FreeType

But I still got the same error:

*** CIRCOS ERROR ***

      cwd: /Users/hao/Project/fujiplot

      command: /Users/hao/Software/circos-0.69-6-kanai/bin/circos -conf

      /Users/hao/Project/fujiplot/config/circos.conf -debug_group summary

  There was a problem with True Type font support. Circos could not render text

  from the font file

      /Users/hao/Software/circos-0.69-6-kanai/bin/../fonts/modern/cmunbmr.ttf

  Please check that gd (system graphics library) and GD (Perl's interface to gd)

  are compiled with True Type support.

  On UNIX systems, try

      gdlib-config --all

  and look for GD_FREETYPE in the 'features' line and -lfreetype in the 'libs'

  line. If these are there, it's likely that your Perl GD module needs

  recompiling.

  For help in installing libgd and/or GD, see

      http://www.perlmonks.org/?node_id=621579

  If you are having trouble debugging this error, first read the best practices

  tutorial for helpful tips that address many common problems

      http://www.circos.ca/documentation/tutorials/reference/best_practices

  The debugging facility is helpful to figure out what's happening under the

  hood

      http://www.circos.ca/documentation/tutorials/configuration/debugging

  If you're still stumped, get support in the Circos Google Group.

      http://groups.google.com/group/circos-data-visualization

  Please include this error, all your configuration, data files and the version

  of Circos you're running (circos -v).Do not email me directly -- please use

  the group.

  Stack trace:

 at /Users/hao/Software/circos-0.69-6-kanai/bin/../lib/Circos/Error.pm line 425.

Circos::Error::fatal_error("font", "no_ttf", "/Users/hao/Software/circos-0.69-6-kanai/bin/../fonts/modern/c"...) called at /Users/hao/Software/circos-0.69-6-kanai/bin/../lib/Circos/Font.pm line 192

Circos::Font::get_label_size("font_file", "/Users/hao/Software/circos-0.69-6-kanai/bin/../fonts/modern/c"..., "size", 10, "text", "abc123") called at /Users/hao/Software/circos-0.69-6-kanai/bin/../lib/Circos/Font.pm line 243

Circos::Font::sanity_check() called at /Users/hao/Software/circos-0.69-6-kanai/bin/../lib/Circos.pm line 726

Circos::run("Circos", "configfile", "/Users/hao/Project/fujiplot/config/circos.conf", "_cwd", "/Users/hao/Project/fujiplot", "_argv", "-conf /Users/hao/Project/fujiplot/config/circos.conf -debug_g"..., "debug_group", ...) called at /Users/hao/Software/circos-0.69-6-kanai/bin/circos line 536

mv: rename /Users/hao/Project/fujiplot/output/circos.png to /Users/hao/Project/fujiplot/output_example/circos.png: No such file or directory

[Junhao Wen]

I was able to successfully run this:

(base)  ✘ MacBook-Pro  ~/Software/circos-0.69-6-kanai/bin  perl gddiag 

allocated 20603 colors

Created color diagnostic image at gddiag.png

GD version 2.77

[Junhao Wen]

The link (http://search.cpan.org/CPAN/authors/id/L/LD/LDS/GD-2.50.tar.gz) did not work for me...

[Junhao Wen]

To install FreeType:

sudo cpanm Font::FreeType 

Password:

Font::FreeType is up to date. (0.16)

[Junhao Wen]

Output for gdlib config:

gdlib-config --all

gdlib-config: warning: this script is deprecated; please use the pkg-config file instead.

GD library  2.2.5

includedir: /usr/local/include

cflags:     -I/usr/local/include

ldflags:     -L/usr/X11/lib

libs:          -lz  -L/usr/local/lib -lpng15    -lfontconfig   -ljpeg   -lXpm -liconv

libdir:     /usr/local/lib

features:   GD_GIF GD_GIFANIM GD_OPENPOLYGON GD_ZLIB GD_PNG GD_FONTCONFIG GD_JPEG GD_XPM

[Martin Krzywinski]

The kind folks at ActiveState have created a Perl build environment for Circos.

https://platform.activestate.com/ReadyMade/Circos/distributions

There's still a couple of bugs to work out and I'll ping here when they're fully baked.

m

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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