Dear List,
as I'm trying to install R and Rgraphwiz on a Fedora Linux, I have a problem
with the environement variable "PKG_CONFIG_PATH". The library "libgvc" is not
getting recognized / found, although a recent version libgvc is on the system
and can be seen via /usr/lib64. I've tried to edit the paths described in
/etc/ldpaths but without any success. Any hints how I can tell the system where
to search for libgvc ?
Thank's in advance,
Wolfgang
Below the complete commands & error message and sessionInfo :
> source("http://www.bioconductor.org/biocLite.R";)
BioC_mirror = http://bioconductor.org
Change using chooseBioCmirror().
> biocLite("Rgraphviz")
Using R version 2.13.0, biocinstall version 2.8.4.
Installing Bioconductor version 2.8 packages:
[1] "Rgraphviz"
Please wait...
trying URL
'http://bioconductor.org/packages/2.8/bioc/src/contrib/Rgraphviz_1.30.1.tar.gz'
Content type 'application/x-gzip' length 730304 bytes (713 Kb)
opened URL
==================================================
downloaded 713 Kb
Welcome to the R installation at the IGBMC !
For news about installation updates (and other related issues) please
subscribe to the 'BioInfoClub' newsgroup at the IGBMC.
You may also have a look at our Wiki at
http://lbgi.igbmc.fr/wikili/index.php/R
If you need additional libraries installed please contact wr...@igbmc.fr
* installing *source* package 'Rgraphviz' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for whether compiler has bool... yes
configure: No --with-graphviz option was specified. Trying to find Graphviz
using other methods.
checking for pkg-config... /usr/bin/pkg-config
Package libgvc was not found in the pkg-config search path.
Perhaps you should add the directory containing `libgvc.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libgvc' found
configure: pkg-config was not able to find the Graphviz library libgvc. This
either indicates that Graphviz is old or that something is wrong. Verify
Graphviz is installed and that PKG_CONFIG_PATH is correct.
checking for dotneato-config... no
configure: dotneato-config not found in PATH.
configure: Using default directory /usr/local, consider specifiying
--with-graphviz
configure: error: /usr/local/bin/dot not found. Check Graphviz installation.
ERROR: configuration failed for package 'Rgraphviz'
* removing '/linux/local/lib64/R/library/Rgraphviz'
The downloaded packages are in
'/tmp/RtmpO9nhoK/downloaded_packages'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package 'Rgraphviz' had non-zero exit status
>
> ##for completeness :
>
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.13.0
>
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
IGBMC,
1 rue Laurent Fries, 67404 Illkirch Strasbourg, France
Tel (+33) 388 65 3300 Fax (+33) 388 65 3276
wolfgang.raffelsberger (at ) igbmc.fr
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