Installation Issues on OS X 10.9 Mavericks

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Hello All,

I know there's been a lot of discussion on this and I have followed numerous threads and website postings as to how to get Circos (or more specifically, Circos' dependencies) installed on Mac OS X to no avail.

I've installed libpng and jpeg (jpeg-8d, specifically).

The problem, of course, is installing GD.

The end output from ./configure for GD is:

** Configuration summary for libgd 2.1.0:

   Support for Zlib:                 yes

   Support for PNG library:          yes

   Support for JPEG library:         yes

   Support for VPX library:          no

   Support for TIFF library:         yes

   Support for Freetype 2.x library: yes

   Support for Fontconfig library:   no

   Support for Xpm library:          no

   Support for pthreads:             yes

configure: creating ./config.status

config.status: creating Makefile

config.status: creating src/Makefile

config.status: creating tests/Makefile

config.status: creating tests/test_config.h

config.status: creating config/Makefile

config.status: creating config/gdlib-config

config.status: creating config/gdlib.pc

config.status: creating src/config.h

config.status: executing depfiles commands

config.status: executing libtool commands

Then, the result of make:

libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/usr/local/include/libpng16 -I/usr/local/Cellar/freetype/2.4.10/include/freetype2 -I/usr/local/Cellar/freetype/2.4.10/include -I/usr/local/Cellar/libtiff/4.0.1/include -g -O2 -fvisibility=hidden -MT gd_jpeg.lo -MD -MP -MF .deps/gd_jpeg.Tpo -c gd_jpeg.c  -fno-common -DPIC -o .libs/gd_jpeg.o

gd_jpeg.c:52:10: fatal error: 'jpeglib.h' file not found

#include "jpeglib.h"

         ^

1 error generated.

make[2]: *** [gd_jpeg.lo] Error 1

make[1]: *** [all] Error 2

make: *** [all-recursive] Error 1

So, the problem seems to be with jpeglib, but I can't figure out what the issue is or how to solve it.

Any insight anyone can give would be greatly appreciated!

Thanks!

james

[Paulo Nuin]

It seems that you are mixing brew installed packages and trying to compile your own. Can’t you install everything with brew?

Also, if you want to try again just point your GD configure to the dir where your jpeglib.h is located with --with-jpeg=DIR

Paulo

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[James Graham]

Hi Paulo,

Thanks for the reply!

I tried installing with brew, but it tries to download libpng from an old location that no longer exists.

My jpeglib.h exists in /usr/local/include/.

Doing ./configure --with-jpeg=/usr/local/include/ does not change the error produced from the make command:

Making all in src

/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-am

/bin/sh ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.   -I/usr/local/include/libpng16   -I/usr/local/Cellar/freetype/2.4.10/include/freetype2 -I/usr/local/Cellar/freetype/2.4.10/include   -I/usr/local/Cellar/libtiff/4.0.1/include    -g -O2 -I/usr/local/include//include -fvisibility=hidden -MT gd_jpeg.lo -MD -MP -MF .deps/gd_jpeg.Tpo -c -o gd_jpeg.lo gd_jpeg.c

libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/usr/local/include/libpng16 -I/usr/local/Cellar/freetype/2.4.10/include/freetype2 -I/usr/local/Cellar/freetype/2.4.10/include -I/usr/local/Cellar/libtiff/4.0.1/include -g -O2 -I/usr/local/include//include -fvisibility=hidden -MT gd_jpeg.lo -MD -MP -MF .deps/gd_jpeg.Tpo -c gd_jpeg.c  -fno-common -DPIC -o .libs/gd_jpeg.o

gd_jpeg.c:52:10: fatal error: 'jpeglib.h' file not found

#include "jpeglib.h"

         ^

1 error generated.

make[2]: *** [gd_jpeg.lo] Error 1

make[1]: *** [all] Error 2

make: *** [all-recursive] Error 1

Thanks again for your reply and if you have any other ideas, I would appreciate them!

james

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[Paulo Nuin]

Did you run brew update? 

And on the make side, did you clean before making again?

Just checking.

Paulo

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[James Graham]

Thanks, Paulo!

I thought I had updated brew, but it seems I hadn't.

I now seem to have everything installed correctly, but now get the conf file error (when doing perl bin/circos ):

  *** CIRCOS ERROR ***

  CONFIGURATION FILE ERROR

  Circos could not find the configuration file. To run Circos, you need to

  specify this file using the -conf flag. The configuration file contains all

  the parameters that define the image, including input files, image size,

  formatting, etc.

[SNIP]

So, that's an improvement!

I get the error even when using the -conf flag and pointing it to etc/circos.conf

When in example/, I run:

perl ../bin/circos -conf etc/circos.conf -debug_group summary,timer > run.out

I get a "There was a problem with True Type font support" in run.out.

So, I guess I need to figure out how to add free type to GD...I know I compiled it with the free type flag, but maybe something funky happened...

Thank you for your help, Paulo!

james

Just checking.

Paulo

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[Paulo Nuin]

Just try installing GD with brew also, if you haven’t done that. Maybe check the archives from the list, I am quite sure people had problems with TT before.

Cheers

Paulo

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[James Graham]

That worked...but now when I run the example, the run.out file says I don't have GD::Polyline installed, but when I try to install it via CPAN (sudo perl -MCPAN -eshell), it says it is already installed (I installed the perl GD module via CPAN, first which should get Polyline, too).

I used force install via CPAN and then it went back to the True Type error...

Argh.

Sorry for all the questions!

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[James Graham]

OK, now when I run gdlib-config --all, I get:

GD library  2.1.0

includedir: /usr/local/include

cflags:     -I/usr/local/include

ldflags:     -L/usr/local/lib

libs:       -ljpeg -lz  -L/usr/local/Cellar/libpng/1.5.14/lib -lpng15 -L/usr/local/Cellar/freetype/2.5.0.1/lib -lfreetype -lz -lbz2 -L/usr/local/Cellar/libtiff/4.0.1/lib -ltiff   -liconv

libdir:     /usr/local/lib

features:   GD_TIFF GD_JPEG GD_FREETYPE GD_PNG GD_GIF GD_GIFANIM GD_OPENPOLYGON

But I am still getting the Circos True Type error...

I am very confused.

james

On Wednesday, November 6, 2013 6:32:19 PM UTC-5, nuin wrote:

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[Paulo Nuin]

No, installing from cpan always fails even when it doesn’t seem like. install Perl’s GD manually.

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[James Graham]

Paulo,

THANK YOU!!!

I am up and running, now!


james

[Paulo Nuin]

Good to hear. Cheers

Paulo