[BioC] Rgraphviz installation problem on " chmod: cannot access '~/library/Rgraphviz/libs/*': No such file or directory"
Robert Gentleman
rgentlem at fhcrc.org
Fri Oct 19 16:38:30 CEST 2007
That version of graphviz is *not* supported in that version of R. You
are one year out of date in your R (and your Linux is pretty old as well
- gcc 4.x.x is what you should be using now a days).
Updating should make solve the problem.
best wishes
Robert
Amin Moghaddasi wrote:
> 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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>>
>
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--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org
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