Question: Rgraphviz installation problem on " chmod: cannot access '~/library/Rgraphviz/libs/*': No such file or directory"
0
gravatar for Amin Moghaddasi
12.1 years ago by
Amin Moghaddasi130 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.
rgraphviz • 872 views
ADD COMMENTlink modified 12.1 years ago by Kasper Daniel Hansen6.4k • written 12.1 years ago by Amin Moghaddasi130
Answer: Rgraphviz installation problem on " chmod: cannot access '~/library/Rgraphviz/li
0
gravatar for Kasper Daniel Hansen
12.1 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor
ADD COMMENTlink written 12.1 years ago by Kasper Daniel Hansen6.4k
Answer: Rgraphviz installation problem on " chmod: cannot access '~/library/Rgraphviz/li
0
gravatar for Tony Chiang
12.1 years ago by
Tony Chiang570
Tony Chiang570 wrote:
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ADD COMMENTlink written 12.1 years ago by Tony Chiang570
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/Rgrap hviz_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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 12.1 years ago by Amin Moghaddasi130
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_U S.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/Rgra phviz_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. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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
ADD REPLYlink written 12.1 years ago by rgentleman5.5k
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