Question

Error installing Rgraphviz

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prochlorothrix • 0

@prochlorothrix-9263

Last seen 8.4 years ago

Sweden

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

installation rgraphviz • 1.8k views

ADD COMMENT • link updated 8.4 years ago by James W. MacDonald 65k • written 8.4 years ago by prochlorothrix • 0

score 1 · Answer 1 · 2015-11-24

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 17 hours ago

United States

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 COMMENT • link 8.4 years ago James W. MacDonald 65k

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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 REPLY • link 8.4 years ago prochlorothrix • 0

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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?