[R] how to define PKG_CONFIG_PATH ?

[Prof Brian Ripley]

On Tue, 31 May 2011, Wolfgang RAFFELSBERGER wrote:

> 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 ?

Which Fedora version does matter here: see the posting guide 
(including for which list to use: not this one!).  But you have not 
most likely not installed the correct RPMs:

gannet% rpm -q --whatprovides /usr/lib64/pkgconfig/libgvc.pc
graphviz-devel-2.26.3-2.fc14.x86_64

on Fedora 14.  Almost certainly you have graphviz but not 
graphviz-devel installed.

On some earlier versions of Fedora you needed to add a library path to 
the ld.so cache.

>
> 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  wraff at 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
>
> 	[[alternative HTML version deleted]]
>
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> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595