Question: (Closed) Problem with Installing some R packages
gravatar for zaynabmousavian
5.4 years ago by
zaynabmousavian10 wrote:


When I have tried to install some R packages such as Rgraphviz, I get the following error:


* installing *source* package 'Rgraphviz' ...

   WARNING: this package has a configure script
         It probably needs manual configuration

** libs
gcc -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -Ilibwin/i386/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC   -O3 -Wall  -std=gnu99 -mtune=core2 -c LL_funcs.c -o LL_funcs.o
gcc: unrecognized option `-std=gnu99'
d:\RCompile\CRANpkg\extralibs64\local\include\.: Permission denied
make.exe: *** [LL_funcs.o] Error 1
Warning: running command 'make -f "" -f "C:/PROGRA~1/R/R-31~1.2/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-31~1.2/share/make/" SHLIB="Rgraphviz.dll" OBJECTS="LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o"' had status 2
ERROR: compilation failed for package 'Rgraphviz'
* removing 'C:/Program Files/R/R-3.1.2/library/Rgraphviz'
Warning messages:
1: running command '"C:/PROGRA~1/R/R-31~1.2/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.1.2\library" "Rgraphviz_2.12.0.tar.gz"' had status 1 
2: In install.packages("Rgraphviz_2.12.0.tar.gz", repos = NULL, type = "source") :
  installation of package ‘Rgraphviz_2.12.0.tar.gz’ had non-zero exit status

I am mostly appreciate any comment.



R • 3.0k views
ADD COMMENTlink written 5.4 years ago by zaynabmousavian10

Hello zaynabmousavian!

We believe that this post does not fit the main topic of this site.

We're not an R forum.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.


ADD REPLYlink written 5.4 years ago by Devon Ryan96k

I need this package for bioinformatic analysis in the RDAVIDWebservice package, and I also have  this problem with some other bioinformatic R packages. 

ADD REPLYlink written 5.4 years ago by zaynabmousavian10

It's still just an R question. If you read the error message you get you'll see that this is likely due to a folder permission needing changed (note the "Permission denied" part).

ADD REPLYlink written 5.4 years ago by Devon Ryan96k
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