So the thing is my IT department is scared of R and therefore only allows us to use it on a laptop that can't go online. Therefore they are the ones to install packages on it.
But due to covid I'm at home discovering they didn't install the requested packages. So I'm looking to see if there is a way to download these packages on a laptop with internet access, add them to an USB and then install them from the USB in R?
Quite easy, just download the package from the CRAN site e.g. https://cran.r-project.org/web/packages/imputeTS/
You can either download the "Package source" or the "Binaries" (must be your operating system.
If you are using R Studio, there is then even a menu item for installing the package - just select the file you downloaded and here you go.
If you are not using R Studio, just provide the path to your downloaded archive in the install.packages command.
The only problem is, you also need all the dependencies ...;)
So you ideally already have them and just one package is somehow missing - otherwise this can get quite time consuming to download all the dependencies - because the dependencies itself also usually have dependencies themselves...
In this case the miniCRAN solution Roland linked in the comments might be an idea. ( Offline installation of a list of packages: getting dependencies in order ) But didn't try the miniCRAN myself yet - would be interested how good this actually works.
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
Let's say I wanted to install a library off of github without devtools. How would I do that?
I was helping a student in office hours today, and devtools required a lot of dependencies. It took nearly a half-an-hour just to get him ready to use it. I know that install.packages works for local files, is the github setup going to enable this?
Let's say: https://github.com/laresbernardo/lares
I understand that devtools::install_github is just a wrapper for remote::install_github which explains some of the dependency issues with these packages (and tidyverse in general - haven was broken today for Windoze).
Can I not install a package directly using install.packages from R:base using the remote source?
In R, I have developed my own package for work (let's call it 'foo') and I have built the package and produced a binary foo.zip with the dependencies (e.g. ggplot2) listed in the description file.
When I use the R package installer in the packages tab it doesn't automatically download the dependencies from CRAN. Ultimately I don't want the end user to have to do this and I don't intend to load it to CRAN for the time being.
I have a way with: devtools::install_dep but I don't want the user to have to do this!
Use the remotes package:
remotes::install_deps("~/RStudio/foo/foo.tar.gz")
You don't say how you're expecting users to install the package. I believe if you put it on the web on a CRAN-like repository, and tell your users to install from there, R will by default install dependencies. This involves telling them how to add your repository to the repository list, so it might be just as easy to ask them to install devtools and use devtools::install_dep.
Another possibility is to distribute your package in a source version; then this answer: https://stackoverflow.com/a/38902163/2554330 gives ideas how to proceed. One that works for me to install something like "~/RStudio/foo/foo.tar.gz" is
install_url(paste0("file://", normalizePath("~/RStudio/foo/foo.tar.gz")))
If you are on Windows, you'll probably need a slightly different way to construct the URL.
Distributing binary packages is only convenient if all your users use the same version of R as you do; they aren't guaranteed to work if the minor version number changes.
When I install the packages in R, sometimes it is used by devtools::install_github(). other times it is used by install.packages().
Could I ask what is the essential difference between them?
R's official repository for packages is located on CRAN (Comprehensive R Archive Network). The process of publishing a package there is very strict and is reachable via install.packages(). For the most part, binary packages (opposed to source code, which is not "properly translated" yet) are available and no additional tools need to be present for proper installation (see next paragraph).
GitHub is one of many webservices that offers repositories for code, incl. R code. Author can upload her or his package and if everything is in its place, the user can install a package from source via devtools::install_github(). This means you need to have a proper toolchain installed (also a distributoin of LaTeX). In Windows, this means Rtools. Linux based OS are likely to be shipped with most of the necessary tools.
Some time ago, you used to be able to install the rcom package in R to use COM scripting (eg, access to external programs.) Unfortunately, it seems to be discontinued:
Package ‘rcom’ was removed from the CRAN repository.
Formerly available versions can be obtained from the archive.
This depends on statconnDCOM, which nowadays restricts use, contrary
to the CRAN policy for a package with a FOSS licence. See
http://rcom.univie.ac.at/ and http://www.statconn.com/.
Following the archive and statconn links and installing one of the older versions in R version 3 gives the error:
“Error: package ‘rcom’ was built before R 3.0.0: please re-install
it”.
I am not very familiar with R, but there seems no way around this message - after all, it occurs when installing, so re-installing doesn't seem to be the answer. It appears as though rcom is simply not available for recent (3.0+) versions of R. I have also scanned the package list, although searching for "COM" there returns over a hundred results and it is possible I missed the right one when clicking through them.
How can I use the rcom package, or use COM from within R some other way?
(Note: I am asking this question on behalf of a colleague. I have no experience with R myself at all. Both of us, when searching for answers, could not find anything. I am sure that others are also using COM in the latest version of R, though!)
I looked at the rcom source code a few months ago. It seems I can get it to build and install OK on R3.0.1. Below is the procedure if it helps.
Get a checkout of the latest source code of rcom. I have rcom_2.2-5.tar.gz locally. I can google something at the following address, but I have no idea of the provenance, so up to you to check it is legit. http://cran.open-source-solution.org/web/packages/rcom/index.html
in R do install.packages('rscproxy')
install Rtools as per the instructions on the R web site (http://cran.r-project.org/bin/windows/Rtools),
open a Windows command prompt i.e. run "CMD"
go to the folder containing the 'rcom' folder, and at the command prompt:
set R="c:\Program Files\R\R-3.0.1\bin\i386\R.exe"
%R% CMD check --no-manual rcom
check it passes without too many complaints. Your call as to the --no-manual option (if you have MiKTeX installed you may remove it)
%R% CMD INSTALL rcom
should result in
installing to c:/Rlib/rcom/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
rcom requires a current version of statconnDCOM installed.
To install statconnDCOM type
installstatconnDCOM()
This will download and install the current version of statconnDCOM
You will need a working Internet connection
because installation needs to download a file.
* DONE (rcom)
in R:
library(rcom)
installstatconnDCOM()
I tried a comRegisterRegistry() ; comRegisterServer()
; x<-comGetObject("Excel.Application") but I get a NULL for x. I am not a user of rcom so while it all seems to compile fine; it may just not work anymore.
If you happen to need to access .NET code, a viable option (and yes I have a vested interest in mentioning it) may be the rClr package.
Hope this helps; I'd be interested to hear how you go.
This really should be a comment, but I don't have enough rep points yet to leave one.
I found that the above steps did not work for me, but the answer posted by Lisa Ann on this question, RExcel in R 3.0.x, did solve my problem installing rcom. Since you need rcom to run RExcel, the initial steps to install RExcel cover installing rcom on newer versions of R (such as 3.0.2).
Specifically, following the advice on statconn's wiki, http://homepage.univie.ac.at/erich.neuwirth/php/rcomwiki/doku.php?id=wiki:how_to_install
You also need to follow these instructions if you upgrade R, i.e. you install a new >release of R after you have installed RExcel.
Download the statconn DCOM server and execute the program you downloaded
Start R as administrator (on Windows 7 you need to right-click the R icon and click the >corresponding item)
In R, run the following commands (you must start R as administrator to do this)
install.packages(c("rscproxy","rcom"),repos="http://rcom.univie.ac.at/download",lib=.Library)
library(rcom)
comRegisterRegistry()
Now you have rcom installed, [instructions for installing RExcel follow...]
New versions of rcom and rscproxy (also for current versions of R) are available from a different repository. Just use http://rcom.univie.ac.at/download as the R repository to install from and you can download and install binary versions of statconn packages from there.
Hope this helps!