The Rcmdr package is a standard R package, and it installs and is loaded in the normal manner. There are, however, a few installation issues, particularly on Macintosh systems, and these are described in this document.
For more detailed basic installation instructions, see Ch. 2 of my book Using the R Commander.
A general point is keep in mind is that the Rcmdr package uses a number of other "contributed" packages (in addition to packages, such as tcltk and MASS, that are part of the standard R distribution), and these must be present for it to work properly. Many of these packages have their own dependencies, which depend on still other packages, etc. These additional packages will either be installed along with the Rcmdr package or the Rcmdr will offer to install them when it first starts up (and you should accept the offer).
The following instructions may be all you need to get started; for more detailed instructions and potential installation issues, see the various sections below. These instructions assume that you have an active Internet connection.
Not really an installation
issue, but a common problem on all platforms: If you save the R
workspace when you exit from R (which, unfortunately, is the
out-of-the-box default at the end of a session on all platforms
and in RStudio), then you can expect to experience problems when
the saved workspace is loaded at the start of subsequent sessions.
The preemptive remedy is never to save the R workspace at the end
of a session. If you do save the workspace on exiting from R, the
remedy is to delete the file in which the workspace is saved,
which is named .RData. Files with
names beginning with a period are (again unfortunately)
generally hidden from the Windows File Explorer and the macOS
Finder. To reveal .RData in Windows File
Explorer, see
these
instructions; in macOS Finder, see
these
instructions. Finally, If you exit from R directly
from the R Commander, the R workspace isn't saved.
Occasionally, an R package or packages required by the Rcmdr package fails to be installed and the R Commander can't start. When this happens, there is typically an informative error message about the missing package(s). There are two common causes for this problem: (1) The package(s) in question may be temporarily missing from the CRAN mirror that you used; or (2) the package(s) may be permanently unavailable for an older version of R.
In the first instance, you can install (each) missing package directly via the command install.packages("package-name"), or, for more than one missing package, install.packages(c("package-1-name", "package-2-name", etc)) , selecting a different CRAN mirror from the one you used initially. In the second instance, you can install the current version of R (always a good idea), and start again.
If you wish to start the R Commander automatically when R starts up, you can add a plain-text ("ascii") file named .Rprofile to your home directory, with the following contents:
local({
old <- getOption("defaultPackages")
options(defaultPackages = c(old, "Rcmdr"))
})
To determine your home directory, type the command getwd() ("get working directory") at the > command prompt in a fresh R session. Be sure to use a plain-text editor to create this file, not a word processor like Word, or, if using a word processor, to save the file as a plain-text file.
If the general installation procedure and installation issues above are insufficient, here is specific information for Windows, Linux, and macOS systems:
The easiest way to install the Rcmdr package is via the Rgui Packages -> Install packages menu or via the command install.packages("Rcmdr") entered at the R > command prompt. R will ask you to select a CRAN mirror; pick the first, "0-Cloud" mirror, or a mirror site near you.
When you first load the Rcmdr package with the command library("Rcmdr"), it will offer to download and install missing dependencies; allow it to do so. If you installed R in Program Files, you may prefer to run R with adminstrator privileges to install packages: Right click the R icon and select "Run as administrator." Otherwise, packages will be installed in a package library particular to your user account rather than the main R package library; that should work OK too. I suggest that you install R into a different directory, such as C:\R\, to avoid this issue.
On Windows, the Rcmdr package works best with the "single-document "R interface (SDI). Under the default "multiple-document interface" (MDI), R Commander dialog boxes may not stay on top of the main R window. In the Startup options screen of the R installer, select Yes (customized startup). Then select the SDI (single-document interface) in preference to the default MDI (multiple-document interface); feel free to make other changes, but you may take all the remaining defaults.
If you install R with the standard MDI, to enable the SDI you can make a copy of the R desktop icon (right-click on the icon, drag it to a different location on the desktop, select Copy Here from the context menu). Right-click the new icon and select Properties. Add --sdi (preceded by a space) to the Target field on the Shortcut tab of the Properties dialog box. The field should read something like "C:\Program Files\R\R-x.y.z\bin\Rgui.exe" --sdi, where x.y.z specifies the version of R you installed. If you wish, change the name of the icon on the General tab (e.g., to R x.y.z SDI). Click OK. Alternatively, you canyou can edit the Rconsole file in R's etc subdirectory to select the SDI.
Linux/Unix systems typically have all of the software required for building packages already installed. The easiest way to install the Rcmdr package is to run R as root and issue the command install.packages("Rcmdr") at the R prompt. R will ask you to select a CRAN mirror; pick the first, "0-Cloud" mirror, or a mirror site near you.
On Ubutu systems, in particular, the following procedure should work (slightly modified from a suggestion by Ista Zahn):
It is also possible to install R and R packages from the Ubuntu package respository but these are almost always out of date.
When you first load the Rcmdr package with the command library(Rcmdr), it will offer to download and install missing dependencies; allow it to do so.
These instructions are for R version 3.6.1 or later; if you're using an earlier version of R, I suggest that you upgrade (in fact, it's generally a good idea to upgrade to the current version of R), or, failing that, consult the special macOS installation notes for the R Commander under older versions of R. R 3.6.1only supports macOS version 10.11 (El Capitan) or higher. Please read these instructions carefully, as they are a little complicated.
Note that if and when you upgrade macOS, you will have to reinstall XQuartz even if you installed it previously.
install.packages("Rcmdr")
(1) You can suppress app nap via the R Commander Tools -> Manage macOS app nap for R.app menu. Select the radio button to set app nap off in the resulting dialog box. This setting is permanent across R.app sessions until you change it.
(2) You can avoid the problem by running R in a terminal window rather than using R.app. There really is no reason to prefer running the R Commander in R.app, so using R from a terminal should be perfectly fine .
(3) You can prevent your computer from napping when R.app is running, even if it's not visible, by right-clicking (or control-clicking) on R.app in the Applications folder in the Finder, and selecting Get Info from the context menu. Check the box next to Prevent App Nap. The change is permanent until you reverse it by unchecking the box. This solution only works with the snowleopard build of R.app.
(4) Enter the following command in a Mac terminal window at the Unix command prompt:
defaults write org.R-project.R NSAppSleepDisabled -bool YES
This is the manual equivalent of solution (1), and is permanent until reversed.
As part of the installation process, XQuartz builds a font cache. Occasionally, the font cache isn't built on installation, and instead the cache is built when the R Commander (and hence XQuartz) is first used. This process can be time-consuming and may initially slow down the performance of the R Commander (with, e.g., dialog boxes taking a long time to display); if this problem occurs, please be patient -- the problem should resolve itself after the font cache is built.
If you are using macOS 10.9 ("Mavericks") or later and the R Commander becomes slow or unresponsive during a session, you can run R and the R Commander in a terminal window on your Mac rather than from R.app or prevent your computer from "napping" while R.app is running. See "Suppressing app nap" in the installation notes above.
Occasionally, the Rcmdr package will fail to load properly in macOS. When this problem occurs, the cause is almost always the failure of the tcltk package to load --The Rcmdr package depends on the tcltk package. You can confirm this diagnosis by trying to load the tcltk package directly, in a fresh R session, issuing the command library(tcltk)at the R command prompt.
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
call: system2("otool", c("-L", shQuote(DLL)), stdout = TRUE)
error: error in running command
Error: package or namespace load failed for ‘tcltk’
sh: otool: command not found
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object
'/Library/Frameworks/R.framework/Versions/3.0/Resources/library/tcltk/libs/tcltk.so':dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/tcltk/libs/tcltk.so,
10): Library not loaded: /usr/X11/lib/libfreetype.6.dylib
Referenced from: /usr/local/lib/libtk8.6.dylib
Reason: Incompatible library version: libtk8.6.dylib requires version
14.0.0 or later, but libfreetype.6.dylib provides version 13.0.0
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object
'/Library/Frameworks/R.framework/Versions/3.0/Resources/library/tcltk/libs/
tcltk.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/tcltk
/libs/tcltk.so, 10): Library not loaded: /usr/local/lib/libtcl8.6.dylib
Referenced from:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/tcltk/libs/t
cltk.so
Reason: no suitable image found. Did find:
/usr/local/lib/libtcl8.6.dylib: stat() failed with errno=13
/usr/local/lib/libtcl8.6.dylib: stat() failed with errno=13
You can verify the source of this problem by issuing the following command at the R command prompt:
system("ls -ld /usr/local /usr/local/lib /usr/local/lib/libtcl*")
If there is a file-permissions problem, you should see something like
ls: /usr/local/lib: Permission denied
ls: /usr/local/lib/libtcl*: Permission denied
drwx------ 8 root wheel 272 Sep 24 10:21 /usr/localHaving confirmed the problem, you can change the file permissions in /usr/local by opening a terminal window on your Mac (Terminal.app is in the Applications Utilities folder), and entering the following command at the $ prompt in the terminal window:
sudo chmod -R a+rX /usr/local
The operating system will ask you to supply your password to execute this command.
Installing R and the Rcmdr package is sufficient for creating HTML (web page) reports via the R Markdown document that the R Commander builds for each session, but if you prefer to create editable Word or Open Office documents or PDF files for reports, you will have additionally to install Pandoc and LaTeX (the latter, in conjunction with Pandoc, for PDF reports). The most convenient way to do this is via the R Commander Tools > Install auxiliary software menu (which appears only if Pandoc or LaTeX is absent).
Last modified: 2023-03-19 by John Fox <john.david.fox AT proton.me>.