[BioC] Rgraphviz installation problem on " chmod: cannot access '~/library/Rgraphviz/libs/*': No such file or directory"

[Kasper Daniel Hansen]

You have an old version of R. You are trying to install an _ancient_  
(like several years old) version of Rgraphviz. You should
1) Preferably update R
2) At the very least use the newest version of Rgraphviz (1.16.0)

Using bioLite.R you almost manage to do it right, but you bang into a  
problem with graphviz 2.14 : their configure script was wrong so some  
header files are not where they are supposed to be (look at the output).

I am not sure whether we have worked around this in Rgraphviz 1.16,  
but you should try.

Kasper

On Oct 19, 2007, at 5:38 AM, Amin Moghaddasi wrote:

> Dear All,
>
> I have some problem installing Rgraphgviz on my system with the
> following specification.
>
> My system is Suse 9.2 , i386 GNU/Linux
> I have installed graphviz-2.14.1 from source
> I have gcc version 3.3.4 (pre 3.3.5 20040809)
> I also set the LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/ 
> graphviz
> R version 2.4.1 (2006-12-18)
>
> 1 - When I try to install from bash command, I'll get the following
> error:
>> R CMD INSTALL Rgraphviz_1.5.0.tar.gz
> * Installing *source* package 'Rgraphviz' ...
> checking for graphviz... checking for dotneato-config... not found
> failed
> configure: error: please specify a valid path to 'dotneato-config'
> version >= 1.12 using --with-graphviz=DIR
> ERROR: configuration failed for package 'Rgraphviz'
> ** Removing '/home/bkp-moghadda/lib/R/library/Rgraphviz'
>
> 2 - using biocLite in R gives another error:
>> source("http://bioconductor.org/biocLite.R")
> Warning messages:
> 1: Redefining ‘biocinstall’ in: safeSource()
> 2: Redefining ‘biocinstall.affyPkgs’ in: safeSource()
> 3: Redefining ‘biocinstall.allPkgs’ in: safeSource()
> 4: Redefining ‘biocinstall.defaultPkgs’ in: safeSource()
> 5: Redefining ‘biocinstall.graphPkgs’ in: safeSource()
> 6: Redefining ‘biocinstall.litePkgs’ in: safeSource()
> 7: Redefining ‘biocinstall.monographPkgs’ in: safeSource()
>> biocLite("Rgraphviz")
> Running biocinstall version 1.9.9 with R version 2.4.1
> Your version of R requires version 1.9 of Bioconductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>          argument 'lib' is missing:
> using /home/bkp-moghadda/lib/R/library
> trying URL
> 'http://bioconductor.org/packages/1.9/bioc/src/contrib/ 
> Rgraphviz_1.12.3.tar.gz'
> Content type 'application/x-gzip' length 1504829 bytes
> opened URL
> ==================================================
> downloaded 1469Kb
>
> * Installing *source* package 'Rgraphviz' ...
> checking for pkg-config... /usr/local/bin/pkg-config
> configure: Found graphviz 2.14.1
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -std=gnu99 -I/usr/lib/R/include -I/usr/lib/R/include
> -I/usr/local/include/graphviz    -DGRAPHVIZ_MAJOR=2 - 
> DGRAPHVIZ_MINOR=14
> -I/usr/local/include    -fpic   -c Rgraphviz.c -o Rgraphviz.o
> In file included from /usr/local/include/graphviz/gvc.h:20,
>                  from common.h:38,
>                  from Rgraphviz.c:1:
> /usr/local/include/graphviz/types.h:27:1: warning: "TRUE" redefined
> In file included from common.h:8,
>                  from Rgraphviz.c:1:
> /usr/lib/R/include/Rdefines.h:148:1: warning: this is the location of
> the previous definition
> In file included from Rgraphviz.c:1:
> common.h:42:20: gvcint.h: No such file or directory
> common.h:43:21: globals.h: No such file or directory
> Rgraphviz.c: In function `getListElement':
> Rgraphviz.c:51: warning: implicit declaration of function  
> `Rf_type2char'
> Rgraphviz.c: In function `Rgraphviz_graphvizVersion':
> Rgraphviz.c:1042: error: dereferencing pointer to incomplete type
> make: *** [Rgraphviz.o] Error 1
> chmod: cannot access
> `/home/bkp-moghadda/lib/R/library/Rgraphviz/libs/*': No such file or
> directory
> ERROR: compilation failed for package 'Rgraphviz'
> ** Removing '/home/bkp-moghadda/lib/R/library/Rgraphviz'
>
> The downloaded packages are in
>         /tmp/Rtmpmnucc7/downloaded_packages
> Warning messages:
> 1: installation of package 'Rgraphviz' had non-zero exit status in:
> install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,
> 2: cannot create HTML package index in:
> tools:::unix.packages.html(.Library)
>
> I would be much appreciated if someone can help me to figure out where
> the problem is.
>
> Regards,
> Amin.
>
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