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I installed XHProf and would like to see call graph visualization. I clicked on View Full Callgraph and got following message first:

failed to execute cmd: " dot -Tpng". stderr: `sh: dot: command not found '

After some googling, I find out, that it's caused by not installed Graphviz. Then I installed it:

$ yum install graphviz

and tried again. Now I'm getting following error messages:

failed to execute cmd: " dot -Tpng". stderr: `Error: /usr/lib64/graphviz/config6 is zero sized, or other read error.

Error: /usr/lib64/graphviz/config6 is zero sized, or other read error.

There is no layout engine support for "dot"

Perhaps "dot -c" needs to be run (with installer's privileges) to register the plugins?

'

Indeed executing of dot -c causes an error:

$ dot -c
Error: /usr/lib64/graphviz/config6 is zero sized, or other read error.
Warning: Could not load "/usr/lib64/graphviz/libgvplugin_pango.so.6" - file not found
Warning: Could not load "/usr/lib64/graphviz/libgvplugin_xlib.so.6" - file not found
Segmentation fault

But the files libgvplugin_pango.so.6 and libgvplugin_xlib.so.6 are there and located in /usr/lib64/graphviz/:

$ ls -l /usr/lib64/graphviz
total 724
...
lrwxrwxrwx 1 root root     26 May 19 13:58 libgvplugin_pango.so.6 -> libgvplugin_pango.so.6.0.0
-rwxr-xr-x 1 root root  22408 Sep 19  2012 libgvplugin_pango.so.6.0.0
lrwxrwxrwx 1 root root     25 May 19 13:58 libgvplugin_xlib.so.6 -> libgvplugin_xlib.so.6.0.0
-rwxr-xr-x 1 root root  15656 Sep 19  2012 libgvplugin_xlib.so.6.0.0

Well, as symlinks. But it should not matter. Anyway, I also tested this case:

mv /usr/lib64/graphviz/libgvplugin_pango.so.6 /usr/lib64/graphviz/libgvplugin_pango.so.6_DEACT
mv /usr/lib64/graphviz/libgvplugin_xlib.so.6 /usr/lib64/graphviz/libgvplugin_xlib.so.6_DEACT
cp /usr/lib64/graphviz/libgvplugin_pango.so.6.0.0 /usr/lib64/graphviz/libgvplugin_pango.so.6
cp /usr/lib64/graphviz/libgvplugin_xlib.so.6.0.0 /usr/lib64/graphviz/libgvplugin_xlib.so.6

No effect, still the same errors.

What is goning wrong here and how to get this working?

Environment: VirtualBox VM with CentOS 6 as guest system.

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automatix
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2 Answers2

2

I've finally got it working.

Short answer:

I guess the yum update or/and perhaps the ann-libs installation might have been the decisive step(-s). But it's just an assumption, therefore I described all the steps, that might be important (s. below).

Detailed answer:

First I tried to install graphviz with related packages:

$ yum install 'graphviz*'

But the installation didn't work:

Error: php56w-common conflicts with php-common-5.3.3-46.el6_6.x86_64
 You could try using --skip-broken to work around the problem
** Found 1 pre-existing rpmdb problem(s), 'yum check' output follows:
cairo-1.8.8-3.1.el6.x86_64 has missing requires of libpixman-1.so.0()(64bit)

Then I tried the same, but added the graphviz-rhel.repo to the repositories before:

$ cd /etc/yum.repos.d/
$ wget http://www.graphviz.org/graphviz-rhel.repo
$ yum list available 'graphviz*'
$ yum install 'graphviz*'

It failed with another error:

Error: Package: graphviz-2.38.0-1.el6.x86_64 (graphviz-stable)
           Requires: libANN.so.1()(64bit)
 You could try using --skip-broken to work around the problem
** Found 1 pre-existing rpmdb problem(s), 'yum check' output follows:
cairo-1.8.8-3.1.el6.x86_64 has missing requires of libpixman-1.so.0()(64bit)

As expected --skip-broken didn't lead to success as well.

After that I did multiple things: yum clean all, yum erase 'graphviz*', ann-libs installation, and yum update:

$ yum clean all
$ yum install 'graphviz*'
$ yum erase 'graphviz*'
$ cd ~/temp/
$ wget http://dl.fedoraproject.org/pub/epel/6/x86_64/ann-libs-1.1.1-4.el6.x86_64.rpm
$ rpm -i ann-libs-1.1.1-4.el6.x86_64.rpm 
$ yum update

Now it works.

automatix
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1

Had the same problem on some RHEL 6 systems and turns out the problem is with hidden dependencies of Graphviz plugins on some X11 libraries, which I was able to get installed by installing the following rpms:

  • libXau
  • libxcb
  • libXext

So, this solved my problem: yum install gtk2 libXau libxcb libXext

behnam
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