I have a windows server that does not allow me to install anything but it allows me to run exe files (Meaning that I cannot simply download the R installation package and install R that way). I want to run R on it and I like to know if it is possible for me to make an R.exe with some packages like ggplot and lattice included?
Do you have any filestore on the server? I can't imagine that you wouldn't have. You can install packages to any directory, which can then be your own personal library. Look at the help(install.packages) and help(library) and there's a lib or lib.loc argument that tells it where to stick it.
If the reason you can't install is because install.packages can't get through the network to CRAN, then download the binary from CRAN, transfer it to the server, and install that way.
Note that I didn't answer your question about building an R exe with bundled packages (here's that answer: "No") because you thought the answer to that question was the solution to your real problem ("I can't install packages"). Always ask a question to your original problem...
I ran across the portable version of R that could do it for me. It generates a folder that can be moved to the new server.
http://sourceforge.net/projects/rportable/
Related
We have a ubuntu linux server in our office which is a air-gapped environment. There is no internet access to external network.
However I would like to install few R packages like ggplot2, Database Connector, dplyr, Tidyverse etc. I have more than 10-15 packages to download
While I cannot write the usual command install.packages("DatabaseConnector"), I have to download the zipped folders from CRAN as shown here.
I am new to R. So, can you help me with my questions given below?
a) Why is there are no files for linux systems? I only see windows binaries and macOS binaries. Which one should I download?
b) Should I download binaries or package source? which one is easy to install?
c) When I download packages like above as zipped file from CRAN like shown here, will the dependencies be automatically downloaded as well? Or should I look at error messages and keep downloading them one by one?
d) Since I work in a Air-gapped environment, what would be the best way to do this process efficiently.
Under linux packages are always installed from source. There are no official binary packages for linux. However, your distro might offer some of them in the official repositories. Ubuntu does. However these tend to be quite old versions and usually limited to a handfull of the most important packages. So, for linux you have to download the source packages. The zip files are for windows and will not work.
You will also need to download all of the dependencies of the packages. For something like tidyverse this will be a huge number. Tracking those by hand is a lot of work. Easiest is probably to use a package like miniCRAN outside of your airgapped system to build a selective copy of CRAN. You can specify the packages you want and the package will download all dependencies. You can then copy the downloaded directories to your server, point install.packages in the right direction and install as usually using install.packages. For details see https://andrie.github.io/miniCRAN/articles/miniCRAN-introduction.html.
You might also run into the problem that your system does not have all of the depencies needed to build all of the packages. Under ubuntu you need for example to install libxml2-dev to be able to install the xml package. For that you need to use the package manager of ubuntu. How to do that on an airgapped system is another issue
I was trying to install the package RINDSEL but I am unable to install it and I keep getting the following error:
Error in install.packages : cannot open the connection
I downloaded the package from:
rindsel_1.0_2.zip | Integrated Breeding Platform
and loaded it from the directory. Other packages from the directory can be installed but just not this one.
Is the package corrupt or could there be any other error?
I would really be grateful for any help. Thanks in advance
Rename the zip file RinSel Software into Rindsel. That's the name specified in the discription file.
Then, you can install the package in R with the command
install.packages("C:/path/to/Rindsel.zip",repos=NULL,type="win.binary")
That works fine... at first (!!!).
Problem with the Rindsel package is. It is quite old. It was build with R 2.13.1. Therefore, if you want to load the library which would be the next step to use the package in R you will get the error:
Problems building package (Error: "package has been build before R-3.0.0")
My suggestion: Contact the authors of the package and ask them if they can either provide the source file that you can build the package by yourself or if they can bundle the Rindsel package with a newer R version.
(Or you could try to hunt down an old R version and see if you can get the thing running with an old R... However, I would not seriously suggest to do that. It would probably result in conflicting dependencies with the other required packages...)
EDIT 15-02-2018: OP asked if one can build an R package with sources that are presumeably the Rindsel source files.
Yes, basically, you could do that. You would have to make a your own description and namespace file and put the source file in the R folder than invoke the command in R to build it....
But it's not neccessary with the script files provided by the link the OP posted.
OP, just run the scripts in R! It's quite easy.
Download the zip-file and extract it on your machine.
Go to that directory. The R command would be
setwd('path/to/your/directory')
Than run the R script, e.g, the KNIndex.r. It's simple:
source('KNIndex.r')
Then the script will run and produce some output / prompts.
For future readers,
I was able to fix the error by running RStudio with administrative privileges to get the command to work.
If that does not fix it, you might wish to try
Installing "r tools" if that is not installed already. That can be downloaded from
https://cran.r-project.org/bin/windows/Rtools/
Download a relevant package that you are trying to install (e.g., tidyverse_1.3.0.zip) from https://cran.rstudio.com/
and install that from local path
It can also be installed directly from the web using install.packages("https://cran.rstudio.com/bin/windows/contrib/4.0/tidyverse_1.3.0.zip")
I had the same problem. R was not able to extract and compile the package files to the default installation directory for some system-specific reasons (not R related).
I was able to fix this by specifying the installation directory of the package lib using:
install.packages("your package", lib = 'path/to your/required/installation/directory')
You can then load the package by specifying the lib.loc option while loading it:
library('your package', lib.loc='path/to your/required/installation/directory')
A better solution:
Create a new environment variable (if you are using windows) R_LIBS_USER with the following directory path/to your/required/installation/directory.
This will change the default installation directory of the packages and make it easier to load and install them without specifying the location everytime.
I have found an old R package with a .zip extension on my PC.
I would like to run it, but I do not have the tar.gz that was used to
create it and I use linux. What are my options?
Few, essentially.
A .zip package for R is almost surely a binary built for Windows so you need to find a suitable Windows computer -- or emulator -- to use it.
So, this can be done this way:
install wine (wine is not an emulator),
install R for Windows, which you download manually from CRAN
install the zip package using the usual commands (install.packages("filename.zip",source=NULL)). You will probably get error messages for the dependencies, but incrementally installing those, it should work.
Problem:
C:\>Rcmd.exe INSTALL --build --library=C:/Users/local_aphalo/Documents/R/win-library/3.0 photobiology
C:\>Rcmd.exe INSTALL --build --library=C:/Users/local_aphalo/Documents/R/win-library/3.0 photobiology_0.2.6.tar.gz
The first command (as used by RStudio) builds a ZIP file that is missing the vignettes.
The second command builds a ZIP that includes the vignettes.
Using R CMD instead of Rcmd.exe makes no difference. The .tar.gz was built immediately before attempting to build the .zip file, from exactly the same source files, from within RStudio (which uses Rcmd.exe build photobiology).
The vignettes are coded in .Snw files using knitr, documentation and NAMESPACE use ROxygen2. The problem happens on all of the packages that I have tried to build, but they are very similarly coded. Only one of them uses Rcpp.
When installing the package for use from within RStudio, installing from .tar.gz installs vignettes just fine. If installing from .zip, whether vignettes get installed or not, depends on whether the .zip files contains them or not (which depends on which of the two commands at the top of this message was used to build the .zip file).
I am using R 3.0.1, and also tried a couple of R 3.0.1 patched builds a few days back. I am mostly using Windows 7 (both 32 bit, and 64 bit), I tried once under Ubuntu 64bit, and the problem is reproducible. I first noticed the problem when using RStudio (0.97 and 0.98) and posted a message in the RStudio forum, but have received no answer in a couple of weeks. I have found at least another relatively old post about this problem in the RStudio website forum, but it has not been answered. Today, I investigated a bit further, and the problem is clearly not related to RStudio, as I can reproduce it through the command line.
The question is: Is this behavior a feature? a bug? or I am missing just an option in the command used?
Of course, I can easily work around the problem at the command line by using the .tar.gz file to build the .zip file, but as I think the preferred way of building a package is by just supplying the package name as argument.
Thanks for any insights on the origin of this problem.
I think this is a feature:
if you're installing from source, vignettes are always built
if you're installing from a binary, they're not built, and will only be available if they were built when the binary was made
This approach means that you can distribute vignettes in binary packages to people who might not be able to build them from source.
The forecast package for R has been updated to version 2.12, but there are currently only windows binarys for 2.11 available on CRAN.
How do I install an R package from the source on Windows?
I know this is an old question but it came up first in my Google search for this same question, even though I knew the answer I just wanted something to copy and paste. Which makes it worth improving the answer for future reference. So here is what works for me:
Install rtools, then:
install.packages(path_to_file, repos = NULL, type="source")
Two answers that may help you avoid the hassle of installing Rtools.
Use http://win-builder.r-project.org/ to build a binary version, download it, and install (using install.packages(...,repos=NULL))
If the package has no binary component (i.e. no src directory with C, C++, or Fortran code that needs to be compiled during installation (not true for forecast, but possibly useful some other time) then simply specifying type="source" within the install.packages call (whether from a repository or a local copy of the source tarball (.tar.gz file)) will install the source package, even on Windows.
Start by reviewing the section on Windows packages in the R Installation and Administration manual, then carefully follow the instructions from The Windows toolset appendix.
I know it's usually bad form to mainly provide links in an answer, but these are links to the canonical references on this topic. I simply link to them rather than summarize their contents, since they should be accurate for the most current R release.
I'm not sure if this is the best way, but I found the following method to work (based in part on the answers above):
1) Download the package .tar
2) Move the package to the directory with your user R libraries (e.g., in my case it was "C:/Users/yourUserName/Documents/R/win-library/3.3")
3) Within Rstudio (or elsewhere, probably), run the command... install.packages("packageName.tar", repos=NULL, type="source")
That worked for me at least. Hope it's helpful!
Download the package *.tar.gz.
make sure you have Rtools installed.
Make sure the R and Rtools paths are added in the environment varialble.
Open a command prompt. Type R CMD INSTALL packagename.tar.gz.
it will work i hope.
To install a package from a .tar.gz file, follow these steps:
Launch R to have the R command prompt
Type: install.packages(<path_to_tar.gz_file>, repos = NULL)
or launch directly:
R CMD INSTALL <path_to_.tar.gz_file>
You need to have R installed but you don't need RTools