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

[Amin Moghaddasi]

Dear Tony, 
Thanks for your quick reply, here is my sessioninfo :

> sessionInfo()
R version 2.4.1 (2006-12-18)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"
"methods"
[7] "base"
>        


Cheers,
Amin.


On Fri, 2007-10-19 at 13:46 +0100, Tony Chiang wrote:
> Hi Amin,
> 
> Can you please send the list the output of your sessionInfo(). It will
> help us to try and reproduce the error you get.
> 
> Best,
> --Tony
> 
> On 10/19/07, Amin Moghaddasi <a.moghaddasi at gmail.com> 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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