I need to install R packages in several nodes (10+) in AWS.
I wont be able to open R shell in each and do install.packages("foo")
This will be done using a configuration management tool like Puppet and it'll be easier if i can do an apt-get installation of R packages automatically.
I found a list of R debian packages here:
http://cran.cnr.berkeley.edu/bin/linux/ubuntu/lucid/
But it does not contain all the packages that i need.
Is there a way to convert any R package and it's internal dependencies to a Debian package similar to the approach used in creating r-cran-*.deb?
Have you looked at http://debian-r.debian.net/ ?
All CRAN (and many other) packages already packaged
You can install packages without starting the R console. You can download the tar.gz packages from the cran website. For example here is the tar.gz for the randomForest package: http://cran.r-project.org/src/contrib/randomForest_4.6-7.tar.gz
R CMD INSTALL ${package}.tar.gz
The cran2deb project claims to do exactly this, turning an R package into a Debian package and noting the correct dependencies.
I haven't used it myself yet.
Related
I'm having a bit of a pickle right now with the package tidyverse, that I need for an assignment on layering maps. I tried installing the package using install.packages("tidyverse") and install.packages ("tidyverse", dependencies = TRUE) but when I ran library(tidyverse) it wasn't installed. I searched online and found that I had an older version of RStudio IDE so I uploaded the latest version (1.3.1056).
After installing the newest version, I reinstalled the package but R tells me the following:
"Rtools is required to build R packages but is not currently
installed".
So, I did it, but the R tells me Rtools package is not available for R version 3.5.3.
What can I do to use tidyverse?
It could be a permissions issue, try setting the directory for where you install R packages/libraries on your computer using libpaths. I have to do this on my work laptop because the university has it set up to store things like this in a tempporary directory on the remote server which isn't desirable.
.libPaths("C:/R")
.libPaths()
I need to install few packages that should be installed with remotes::install_github() like
"acidgenomics/basejump" or "satijalab/seurat".
During the installation, it need to upgrade few other packages version. The BiocManager::install program cannot find those versions and I had to install those dependencies packages version with:
R CMD INSTALL IRanges_2.20.2.tar.gz
Then other packages, that use the same packages stop working. like DESeq2,
I get the error:
Error: package or namespace load failed for ‘DESeq2’:
objects ‘rowSums’, ‘colSums’, ‘rowMeans’, ‘colMeans’ are not exported by 'namespace:S4Vectors'
I found few answers that say it happen (like url)
remotes::install_github() isn't picking up the correct Bioconductor
devel repos, whereas installing with BiocManager::install() does work
as expected.
we have the R 3.6.0 installed as a module and a lot of users uses the same R version. I need all packages to work for everyone.
How can I make all variety packages versions to work?
Finally, I install new version of R 3.6.3 with Bioconductor 3.10 and all the packages install right.
I came across a package that is not available on CRAN. I tried to install the package using:
Packages & Data > Package Installer > Local Binary Package > At User
Level > [FileName.tgz] > Install...
This didn't work and I am now trying to use the R CMD INSTALL command. However, it seems I need to run that command in the command line interface but I cannot get it to install properly.
The package I'm trying to install is called gEcon. It can be found here. In particular, I am getting the following error message after "installing" the package:
Error: package or namespace load failed for ‘gEcon’:
package ‘gEcon’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
I assume it's the way I'm installing it.
Thanks in advance.
You're going to need to install Xcode apparently, because you've got to install this from source per these directions:
Now, you've gotta update R to the latest stable release, or if you prefer you can find the exact minimum newest version needed for gEcon.
After upgrading R you can complete the installation from source.
Original answer to original question:
Two things:
To access the command line and use R CMD on an Apple computer, please use the terminal.app app. Please see this for more details.
An easier and probably better approach is to install your package from the author's Github (or BitBucket, etc) repository using devtools::install_github or just use devtools::install on the downloaded source project.
I have a code to track objects in the images. This code uses few function from the package clue. So clue is already installed in my system. Now I have created a package using the same code.
My description file has following lines.
Depends: R (>= 3.4.3),
clue
Because clue is already installed, I thought it will not get installed again when I use install("mypackage"). But to my surprise it re-installed the package. I have tried this with other installed packages, too. When I give it as "depends" or "import", it re-installs the packages. I do not want to re-install the packages if they are already on my system. Is there a way to tell R package installer to avoid re-installing packages that exist on the user's system? Some of these packages are quite large and take a lot of time to install. In addition, I have installed some packages with binary source/dependency that required me to give path for several libraries.
You can just use
install.packages(..., dependencies = FALSE)
or if you use devtools::install:
install(..., dependencies = FALSE)
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.
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.
I think this merits an answer rather than a comment.
A gentleman at Bioconductor helped me get Rgraphviz installed. The primary problem was that the version of Rgraphviz I had downloaded only seems to work with the 32-bit version of R and I was running a 64-bit version of R. I was able to install Rgraphviz in the 32-bit version of R.
I had also made an error or two in the PATH statement during some of my attempts to install Rgraphviz. However, the post above in my second comment provides the instructions for installation.
You just, it seems, cannot install the normal download version of Rgraphviz in the 64-bit version of R.
I think many of our emails back and forth are now posted on the Bioconductor forum.
I might edit this answer with more detailed instructions in the next 24-hours.