Question

I was trying to run code that required the R packages ‘pkgDepTools’ and ‘Rgraphviz’. I received error messages saying that neither package is available for R version 2.15.0.

A Google search turned up the following webpage RPM Pbone that seems to have the packages:

http://rpm.pbone.net/index.php3/stat/4/idpl/17802118/dir/mandrake_other/com/R-pkgDepTools-1.20.0-1-mdv2012.0.i586.rpm.html

and

http://rpm.pbone.net/index.php3/stat/4/idpl/17802080/dir/mandrake_other/com/R-Rgraphviz-1.32.0-2-mdv2012.0.i586.rpm.html

However, the files have an *.rpm extension rather than the *.tar.gz or *.zip extensions I am used to.

I am using Windows 7 and R version 2.15.0. Can I install an R package from an *.rpm file?

From Wikipedia *.rpm seems like maybe it is more for Linux:

http://en.wikipedia.org/wiki/RPM_Package_Manager

Regarding other possible solutions, I have found several earlier posts here with similar questions about installing R packages that are not available for the most recent version of R:

Bivariate Poisson Regression in R?

Package ‘GeneR’ is not available

R Venn Diagram package Venerable unavailable – alternative package?

I have installed the latest version of Rtools and the package ‘devtools’. Although I know nothing about them.

There is an archived version of ‘Rgraphviz’ here:

http://cran.r-project.org/src/contrib/Archive/Rgraphviz/

but I cannot locate an archived version of ‘pkgDepTools’.

If I can install the packages on a Windows machine using the above *.rpm files could someone please provide instructions?

If I must use Rtools to build them I might ask more questions because the instructions at the link below are challenging for me:

http://cran.r-project.org/doc/manuals/R-admin.html#Building-from-source

To be completely transparent I am hoping someone might build them for me, if that is possible. Although I recognize the experience and knowledge gained from doing it myself would probably pay off in the long run.

Thank you for any advice.

Answer 1

pkgDepTools and Rgraphviz are BioConductor R packages not ones hosted on CRAN. Unless you configure your R to download packages from those repos, R will report that they are not available; it can only install from repos it has been configured to install from.

To install those BioConductor packages a lite installation method is provided:

source("http://bioconductor.org/biocLite.R")
biocLite(c("pkgDepTools", "Rgraphviz"))

Further details are provided on the Install page of the BioConductor website

In general you can’t use rpm packages on Windows; rpm’s are the equivalent of a binary package for Linux. Any C/C++/Fortran/etc code will have been compiled for Linux not Windows. If a package really isn’t available for your version of R then check if there is a reason stated on CRAN (usually Windows binaries take a few days longer to produce or there may be requirements for software not available on the CRAN Windows build machines). You can try the WinBuilder service run by Uwe Ligges to build Windows Binaries of packages for you, but if the package was on CRAN and now isn’t that suggests it no longer works with current R and can not be built.

In general try a wider search for packages; the first hit in my Google search results under the search string “pkgDepTools” is the Bioconductor page for the package which includes a link to the Windows binary and instructions on how to install the package from within R.