Question: Error installing Rgraphviz
0
gravatar for prochlorothrix
3.9 years ago by
Sweden
prochlorothrix0 wrote:

Hi!

I'm trying to install Rgraphviz on R version 3.2.2 under Xubuntu 15.04. I always get the following error:

> install.packages("~/Dropbox/Rgraphviz_2.14.0.tar.gz", repos = NULL, type = "source")
Installing package into ‘/home/gibraa/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
* installing *source* package ‘Rgraphviz’ ...
ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual'
* removing ‘/home/gibraa/R/x86_64-pc-linux-gnu-library/3.2/Rgraphviz’
Warning in install.packages :
  installation of package ‘/home/gibraa/Dropbox/Rgraphviz_2.14.0.tar.gz’ had non-zero exit status
 

I unsuccessfully tried different workarounds.  Any suggestion?

Thank you

rgraphviz installation • 896 views
ADD COMMENTlink modified 3.9 years ago by James W. MacDonald51k • written 3.9 years ago by prochlorothrix0
Answer: Error installing Rgraphviz
1
gravatar for James W. MacDonald
3.9 years ago by
United States
James W. MacDonald51k wrote:

It looks like a permissions issue. Rgraphviz has a configure script that isn't executable, likely because it doesn't have the execute bit set. But it looks like you are doing lots of extra work to get the package; putting it into Dropbox, then trying to install from there. Have you tried just doing the 'regular' installation?

library(BiocInstaller)
biocLite("Rgraphviz")

 

ADD COMMENTlink written 3.9 years ago by James W. MacDonald51k

Yes I tried the regular installation first and then the one from source that I reported (just because it produced a shorter output). The error was the same in both cases. I agree it's a permission issue but don't know what to do about.

ADD REPLYlink written 3.9 years ago by prochlorothrix0
1

I downloaded the file to a temporary location

> download.packages("Rgraphviz", repos=BiocInstaller::biocinstallRepos(), "/tmp")
trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/Rgraphviz_2.14.0.tar.gz'
Content type 'application/x-gzip' length 7694656 bytes (7.3 MB)
==================================================
downloaded 7.3 MB

     [,1]        [,2]                          
[1,] "Rgraphviz" "/tmp/Rgraphviz_2.14.0.tar.gz"
> 

and then in the shell 

/tmp$ tar xzf Rgraphviz_2.15.0.tar.gz 
/tmp$ ls -l Rgraphviz/configure
-rwxr-xr-x 1 mtmorgan martin 150702 Jul 30 15:08 Rgraphviz/configure

where -rwxr-xr-x says  that the configure file has it's executable bit set.

/tmp$ R CMD INSTALL Rgraphviz

is successful. If I chmod -x Rgraphviz/configure, and try to R CMD INSTALL Rgraphviz, then I get the error you indicate above. Are you trying to install the software under a restricted user, or from a device that somehow does not allow executable code?

ADD REPLYlink written 3.9 years ago by Martin Morgan ♦♦ 23k

That worked for me as well. Thank you!

ADD REPLYlink written 3.9 years ago by prochlorothrix0
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