Rgraphviz on Fedora Core 6
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@byron-wallace-2018
Last seen 7.7 years ago
Hi all -- I'm having problems installing Rgraphviz on Fedora 6 core. Below is the command line interaction, if anyone has any insight I would greatly appreciate it. Thank you. [CARMA at d-p-13-16 R-Install]$ su root R CMD INSTALL Rgraphviz_1.10.0.tar.gz * Installing *source* package 'Rgraphviz' ... checking for graphviz... checking for dotneato-config... not found checking for pkg-config... /usr/bin/pkg-config configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -I/usr/lib/R/include -I/usr/lib/R/include -I/usr/include/graphviz -DGRAPHVIZGT_2_4 -I/usr/local/include -fpic -O3 -g -std=gnu99 -c Rgraphviz.c -o Rgraphviz.o In file included from common.h:29, from Rgraphviz.c:1: /usr/include/graphviz/gvcint.h:30: error: expected specifier-qualifier-list before 'gvlayout_engine_t' /usr/include/graphviz/gvcint.h:37: error: expected specifier-qualifier-list before 'gvtextlayout_engine_t' /usr/include/graphviz/gvcint.h:91: error: expected specifier-qualifier-list before 'gvevent_key_binding_t' Rgraphviz.c: In function 'getNodeLayouts': Rgraphviz.c:801: error: 'struct <anonymous>' has no member named 'line' Rgraphviz.c:802: error: 'struct <anonymous>' has no member named 'line' Rgraphviz.c:804: error: 'struct <anonymous>' has no member named 'line' Rgraphviz.c:808: error: 'struct <anonymous>' has no member named 'line' Rgraphviz.c: In function 'getEdgeLocs': Rgraphviz.c:930: error: 'struct <anonymous>' has no member named 'line' Rgraphviz.c:941: error: 'struct <anonymous>' has no member named 'line' Rgraphviz.c:945: error: 'struct <anonymous>' has no member named 'line' Rgraphviz.c: In function 'Rgraphviz_graphvizVersion': Rgraphviz.c:986: error: 'GVC_t' has no member named 'info' make: *** [Rgraphviz.o] Error 1 chmod: cannot access `/home/CARMA/R/library/Rgraphviz/libs/*': No such file or directory ERROR: compilation failed for package 'Rgraphviz' ** Removing '/home/CARMA/R/library/Rgraphviz' -- - Byron C. Wallace
Rgraphviz Rgraphviz • 934 views
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@lilongisb-sibch-1725
Last seen 7.7 years ago
Hi, My guess is that you are trying to install a very old Rgraphviz package (bioconductor 1.8?) with the latest graphviz release... I don't think it has anything to do with Fedora 6 core. You could try to install Rgraphviz-1.12.3 which has been updated to work with latest graphviz release. Or try to find a download for an old graphviz, probably 2.8 or so. Li > Hi all -- I'm having problems installing Rgraphviz on Fedora 6 core. > Below is the command line interaction, if anyone has any insight I > would greatly appreciate it. Thank you. > > [CARMA at d-p-13-16 R-Install]$ su root R CMD INSTALL Rgraphviz_1.10.0.tar.gz > * Installing *source* package 'Rgraphviz' ... > checking for graphviz... checking for dotneato-config... not found > checking for pkg-config... /usr/bin/pkg-config > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > gcc -I/usr/lib/R/include -I/usr/lib/R/include -I/usr/include/graphviz > -DGRAPHVIZGT_2_4 -I/usr/local/include -fpic -O3 -g -std=gnu99 -c > Rgraphviz.c -o Rgraphviz.o > In file included from common.h:29, > from Rgraphviz.c:1: > /usr/include/graphviz/gvcint.h:30: error: expected > specifier-qualifier-list before 'gvlayout_engine_t' > /usr/include/graphviz/gvcint.h:37: error: expected > specifier-qualifier-list before 'gvtextlayout_engine_t' > /usr/include/graphviz/gvcint.h:91: error: expected > specifier-qualifier-list before 'gvevent_key_binding_t' > Rgraphviz.c: In function 'getNodeLayouts': > Rgraphviz.c:801: error: 'struct <anonymous>' has no member named 'line' > Rgraphviz.c:802: error: 'struct <anonymous>' has no member named 'line' > Rgraphviz.c:804: error: 'struct <anonymous>' has no member named 'line' > Rgraphviz.c:808: error: 'struct <anonymous>' has no member named 'line' > Rgraphviz.c: In function 'getEdgeLocs': > Rgraphviz.c:930: error: 'struct <anonymous>' has no member named 'line' > Rgraphviz.c:941: error: 'struct <anonymous>' has no member named 'line' > Rgraphviz.c:945: error: 'struct <anonymous>' has no member named 'line' > Rgraphviz.c: In function 'Rgraphviz_graphvizVersion': > Rgraphviz.c:986: error: 'GVC_t' has no member named 'info' > make: *** [Rgraphviz.o] Error 1 > chmod: cannot access `/home/CARMA/R/library/Rgraphviz/libs/*': No such > file or directory > ERROR: compilation failed for package 'Rgraphviz' > ** Removing '/home/CARMA/R/library/Rgraphviz' > > > -- > - Byron C. Wallace > > _______________________________________________ > 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 >
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Thank you so much! You were exactly right about bioconductor 1.8, and I resolved the issue by installing graphviz 2.8. However, I've unfortunately encountered another issue. After I succesfully install both 'graph_1.10.6' and 'Rgraphviz_1.10.0', I start R (v 2.4) and attempt to run the install script to install all the needed bioconductor packages. Here I get an error telling me that the graph library is not installed (see below). I'm lost because I the R CMD INSTALL for the graph library completes successfully. Any insight here? Thank you again for your time. > source("install.R") > install() checking for installed packages... checking for graph: ...Error in install() : ERROR: library graph not installed! install graph package before running this script! In addition: Warning message: there is no package called 'graph' in: library(package, lib.loc = lib.loc, character.only = TRUE, logical = TRUE, On 1/29/07, Li.Long at isb-sib.ch <li.long at="" isb-sib.ch=""> wrote: > > Hi, > > My guess is that you are trying to install a very old Rgraphviz package > (bioconductor 1.8?) with the latest graphviz release... I don't think it > has anything to do with Fedora 6 core. > > You could try to install Rgraphviz-1.12.3 which has been updated to work > with latest graphviz release. Or try to find a download for an old > graphviz, probably 2.8 or so. > > Li > > > > > Hi all -- I'm having problems installing Rgraphviz on Fedora 6 core. > > Below is the command line interaction, if anyone has any insight I > > would greatly appreciate it. Thank you. > > > > [CARMA at d-p-13-16 R-Install]$ su root R CMD INSTALL Rgraphviz_1.10.0.tar.gz > > * Installing *source* package 'Rgraphviz' ... > > checking for graphviz... checking for dotneato-config... not found > > checking for pkg-config... /usr/bin/pkg-config > > configure: creating ./config.status > > config.status: creating src/Makevars > > ** libs > > gcc -I/usr/lib/R/include -I/usr/lib/R/include -I/usr/include/graphviz > > -DGRAPHVIZGT_2_4 -I/usr/local/include -fpic -O3 -g -std=gnu99 -c > > Rgraphviz.c -o Rgraphviz.o > > In file included from common.h:29, > > from Rgraphviz.c:1: > > /usr/include/graphviz/gvcint.h:30: error: expected > > specifier-qualifier-list before 'gvlayout_engine_t' > > /usr/include/graphviz/gvcint.h:37: error: expected > > specifier-qualifier-list before 'gvtextlayout_engine_t' > > /usr/include/graphviz/gvcint.h:91: error: expected > > specifier-qualifier-list before 'gvevent_key_binding_t' > > Rgraphviz.c: In function 'getNodeLayouts': > > Rgraphviz.c:801: error: 'struct <anonymous>' has no member named 'line' > > Rgraphviz.c:802: error: 'struct <anonymous>' has no member named 'line' > > Rgraphviz.c:804: error: 'struct <anonymous>' has no member named 'line' > > Rgraphviz.c:808: error: 'struct <anonymous>' has no member named 'line' > > Rgraphviz.c: In function 'getEdgeLocs': > > Rgraphviz.c:930: error: 'struct <anonymous>' has no member named 'line' > > Rgraphviz.c:941: error: 'struct <anonymous>' has no member named 'line' > > Rgraphviz.c:945: error: 'struct <anonymous>' has no member named 'line' > > Rgraphviz.c: In function 'Rgraphviz_graphvizVersion': > > Rgraphviz.c:986: error: 'GVC_t' has no member named 'info' > > make: *** [Rgraphviz.o] Error 1 > > chmod: cannot access `/home/CARMA/R/library/Rgraphviz/libs/*': No such > > file or directory > > ERROR: compilation failed for package 'Rgraphviz' > > ** Removing '/home/CARMA/R/library/Rgraphviz' > > > > > > -- > > - Byron C. Wallace > > > > _______________________________________________ > > 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 > > > > -- - Byron C. Wallace
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 7.7 years ago
"Byron Wallace" <byron.wallace at="" tufts.edu=""> writes: > Hi all -- I'm having problems installing Rgraphviz on Fedora 6 core. > Below is the command line interaction, if anyone has any insight I > would greatly appreciate it. Thank you. You didn't tell us your version of R. With the current released version of R (2.4.1) you should be able to install Rgraphviz using biocLite (see the BioC homepage). > [CARMA at d-p-13-16 R-Install]$ su root R CMD INSTALL > Rgraphviz_1.10.0.tar.gz The current release of Rgraphviz is 1.12.3 and is intended to be used with R 2.4.x. + seth
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@lilongisb-sibch-1725
Last seen 7.7 years ago
Hi, I think BioConductor 1.8 goes with R 2.3, BioConductor 1.9 goes with R 2.4. There are potential compatability issues if you want to mix the different versions of them... Apart from that, I would double check if R in your "R CMD INSTALL" is the same R as your R 2.4. When they are different, the packages installed from "CMD INSTALL" will be in different places. That'll be a possibility to get what you get. Li > Thank you so much! You were exactly right about bioconductor 1.8, and > I resolved the issue by installing graphviz 2.8. However, I've > unfortunately encountered another issue. After I succesfully install > both 'graph_1.10.6' and 'Rgraphviz_1.10.0', I start R (v 2.4) and > attempt to run the install script to install all the needed > bioconductor packages. Here I get an error telling me that the graph > library is not installed (see below). I'm lost because I the R CMD > INSTALL for the graph library completes successfully. Any insight > here? Thank you again for your time. > >> source("install.R") >> install() > checking for installed packages... > checking for graph: ...Error in install() : > ERROR: library graph not installed! install graph package before > running this script! > In addition: Warning message: > there is no package called 'graph' in: library(package, lib.loc = > lib.loc, character.only = TRUE, logical = TRUE, > > > > On 1/29/07, Li.Long at isb-sib.ch <li.long at="" isb-sib.ch=""> wrote: >> >> Hi, >> >> My guess is that you are trying to install a very old Rgraphviz package >> (bioconductor 1.8?) with the latest graphviz release... I don't think >> it >> has anything to do with Fedora 6 core. >> >> You could try to install Rgraphviz-1.12.3 which has been updated to work >> with latest graphviz release. Or try to find a download for an old >> graphviz, probably 2.8 or so. >> >> Li >> >> >> >> > Hi all -- I'm having problems installing Rgraphviz on Fedora 6 core. >> > Below is the command line interaction, if anyone has any insight I >> > would greatly appreciate it. Thank you. >> > >> > [CARMA at d-p-13-16 R-Install]$ su root R CMD INSTALL >> Rgraphviz_1.10.0.tar.gz >> > * Installing *source* package 'Rgraphviz' ... >> > checking for graphviz... checking for dotneato-config... not found >> > checking for pkg-config... /usr/bin/pkg-config >> > configure: creating ./config.status >> > config.status: creating src/Makevars >> > ** libs >> > gcc -I/usr/lib/R/include -I/usr/lib/R/include -I/usr/include/graphviz >> > -DGRAPHVIZGT_2_4 -I/usr/local/include -fpic -O3 -g -std=gnu99 -c >> > Rgraphviz.c -o Rgraphviz.o >> > In file included from common.h:29, >> > from Rgraphviz.c:1: >> > /usr/include/graphviz/gvcint.h:30: error: expected >> > specifier-qualifier-list before 'gvlayout_engine_t' >> > /usr/include/graphviz/gvcint.h:37: error: expected >> > specifier-qualifier-list before 'gvtextlayout_engine_t' >> > /usr/include/graphviz/gvcint.h:91: error: expected >> > specifier-qualifier-list before 'gvevent_key_binding_t' >> > Rgraphviz.c: In function 'getNodeLayouts': >> > Rgraphviz.c:801: error: 'struct <anonymous>' has no member named >> 'line' >> > Rgraphviz.c:802: error: 'struct <anonymous>' has no member named >> 'line' >> > Rgraphviz.c:804: error: 'struct <anonymous>' has no member named >> 'line' >> > Rgraphviz.c:808: error: 'struct <anonymous>' has no member named >> 'line' >> > Rgraphviz.c: In function 'getEdgeLocs': >> > Rgraphviz.c:930: error: 'struct <anonymous>' has no member named >> 'line' >> > Rgraphviz.c:941: error: 'struct <anonymous>' has no member named >> 'line' >> > Rgraphviz.c:945: error: 'struct <anonymous>' has no member named >> 'line' >> > Rgraphviz.c: In function 'Rgraphviz_graphvizVersion': >> > Rgraphviz.c:986: error: 'GVC_t' has no member named 'info' >> > make: *** [Rgraphviz.o] Error 1 >> > chmod: cannot access `/home/CARMA/R/library/Rgraphviz/libs/*': No such >> > file or directory >> > ERROR: compilation failed for package 'Rgraphviz' >> > ** Removing '/home/CARMA/R/library/Rgraphviz' >> > >> > >> > -- >> > - Byron C. Wallace >> > >> > _______________________________________________ >> > 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 >> > >> >> > > > -- > - Byron C. Wallace >
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 7.7 years ago
"Byron Wallace" <byron.wallace at="" tufts.edu=""> writes: > Thank you so much! You were exactly right about bioconductor 1.8, and > I resolved the issue by installing graphviz 2.8. Not sure how this resolves your issues. > However, I've unfortunately encountered another issue. After I > succesfully install both 'graph_1.10.6' and 'Rgraphviz_1.10.0', I > start R (v 2.4) and attempt to run the install script to install all > the needed bioconductor packages. Here I get an error telling me > that the graph library is not installed (see below). I'm lost > because I the R CMD INSTALL for the graph library completes > successfully. Any insight here? Thank you again for your time. R has a default location for installing packages. The -l argument to R CMD INSTALL will change the default. The environment variable R_LIBS will also override. From inside R, you can see what paths are searched for packages using .libPaths(). It seems likely that you have a mismatch in some way between where you installed and where R is looking. >> source("install.R") >> install() > checking for installed packages... > checking for graph: ...Error in install() : > ERROR: library graph not installed! install graph package before > running this script! > In addition: Warning message: > there is no package called 'graph' in: library(package, lib.loc = > lib.loc, character.only = TRUE, logical = TRUE, what's install.R? I would recommend using biocLite to install the packages you want: Start R and then... souce("http://bioconductor.org/biocLite.R") biocLite("Rgraphviz") + seth
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