Using R version 4.1.2 on Ubuntu 20.04, I run hist(10). The error says
X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 2 at size 14 could not be loaded
I find two things on google. This thread I can't understand, and this thread suggests I build R differently. I did recently build R from source, without the cairo flag recommended by the Bio-Deago github thread, but I have now replaced it with a binary from Rstudio, and the problem persists. Any suggestions? Thanks!
EDIT: the problem only occurs in Rstudio, not when I run R through a terminal.
R gets installed to different places depending on whether you install from source or as a binary: see this, which says:
For versions of R installed by system package managers (e.g. r-base on Debian or Ubuntu) this will be /usr/bin/R. For versions of R installed from source this will typically (but not always) be /usr/local/bin/R.
Rstudio looks first at which R, which in this case is the version from source. I deleted the source version (target of symlink at which R). Then when I ran R in a terminal, said R is not installed. Then, I followed the Rstudio binary install instructions mentioned in the question. I followed them from the beginning even though I had already installed an Rstudio binary. Now I can run hist(10) and get a plot as expected.
Related
I feel pretty comfortable working with R, and I want to get into Python through Anaconda.
Upon trying the Jupyter Notebook and finding it has compatibility with R, I really want to use it.
I'm having problem installing the R packages that don't come in R-essentials; and mainly because I noticed it uses a different R installation than the one I had before. Not only is this a different R installation, but it also uses a previous version of R. In my local installation I have updated to 3.2.3 but in the Anaconda environment for Jupyter I got 3.1.
I also found a post to change the .libPaths variable to include the packages that I had already installed. Still, I see this as a potential problem because of the different R versions.
I wanted to know if I can update the R version that's used in Anaconda, or if I can point to the one that's installed locally.
Thank you.
You can install IRkernel in the normal R installation and then register the kernel: simply follow the instructions at http://irkernel.github.io/installation/
I have been having some weird issues with R (3.1.1) and RStudio (0.98.1079) and I suspect that it is due to the fact that these programs are not longer referencing the right places after I upgraded to Mac OSX 10.10.
In particular, I cannot seem to find packages that I know I have installed on my computer to run using the system command in the R console. That is, running man pdflatex in a Terminal window yields the help manual for PDFLATEX. However running system('man pdflatex') from the R console yields the error message No manual entry for pdflatex.
The issue persists even though I reinstalled R, RStudio and MacTex since I upgraded to Mac OSX 10.10. Any help would be appreciated!
Yosemite has a bug wherein some environment variables, including PATH, appear twice in a program's environment with different values. For instance, you might notice that Sys.getenv("PATH") will show you one PATH, and system("echo $PATH") will show you an entirely different one.
I expect that most of your problems are due to this bug.
There are a few workarounds you can try immediately:
You can manually forward PATH yourself. Try this:
> system2("man", "pdflatex", env=paste0("PATH=", Sys.getenv("PATH")))
Or, you can start RStudio from Terminal:
$ open /Applications/RStudio.app
Both the R and RStudio engineers have implemented workarounds in the last few days. R (as of 3.1.2) and RStudio (as of 0.98.1087) should behave as you'd expect.
There are a host of questions about similar problems. All of them appear to come up when you update OS X to either Yosemite or Sierra with an older version of R already installed.
The easiest solution is to completely uninstall R (note the comments about using which R !), and then to install it again.
This also solves problems such as R showing different version numbers in terminal and the GUI.
I just made the switch from Windows to Ubuntu. In windows I had the possibility to change the R version used in Rstudio IDE with Tools -> Global options -> R versions.
This is not possible in Ubuntu in the same way, indeed the R versions menu does not appear in Ubuntu version of RStudio (why??). Could you help me in finding the good solution for switching among different, already installed versions of R, in Ubuntu?
The switch among different versions is important for satisfying packages modifications and making old scripts working.
I apologize was not a great question, but more of the kind: "please help me, I'm desperate, I've loose all my Windows habs!" ;)
So if anyone like me want to make the switch from Windows to Ubuntu here is how you can compile an older R version and switch between versions using RStudio. As already #Andrie commented out here are some informations, however not complete https://support.rstudio.com/hc/en-us/articles/200486138-Using-Different-Versions-of-R.
You already have the R version provided by Ubuntu Software Center or a more recent version but you need an older version to run an old important script?
First you need to compile the desired R version from source. In Ubuntu updating R to a newer version leave you with one only version (the updated ones) and not two the older and the new like in Win.
Let's go to the shell and install all you need to build R from source
sudo apt-get build-dep r-base
to install all libraries you will need for compiling. (look also here http://cran.us.r-project.org/bin/linux/ubuntu/)
Download the version you need on CRAN
/bin/linux/ubuntu/MyUbuntu(trusty,precise,lucid) The archive you
need is something like:
r-base_TheVersionIWant.orig.tar.gz
Extract it in a directory (maybe ~/R)
then (in the shell) enter the top directory of the unpacked archive
then you can read the INSTALL file, and run configure with the --enable-R-shlib option (otherwise you will not be able once compiled to run it in RStudio)
./configure --enable-R-shlib && make
then following the INSTALL file
make check
make pdf
make info
If all was ok, you can tell R studio where find the bin/R file it needs
export RSTUDIO_WHICH_R= myPahtTo/bin/R
and fire rstudio with
rstudio
You have an RStudio version running the desired R Version.
When you will close the terminal and the rstudio session you will come back to the system default version of R. Then repeat just the last two lines to come back when you want.
After installing Mavericks on my Mac, I'm not able to run Rattle anymore.
Because of compatibility issues between RStudio and 10.9 (http://www.r-bloggers.com/rstudio-and-os-x-10-9-mavericks/), I installed v 0.98.433 of RStudio and R 3.0.2
Tried to launch Rattle the normal way: none.
I tried in a different way:
I manually launched xQuartz to install GTK+
via R-Studio I installed RGtg2 and Cairo
Installed Rattle, launched it and I got 1 sec message from Rattle, before it disappeared, crashing R session.
I then tried going back to R 2.15.3 (using RSwitch), doing same procedure.
Rattle starts with no ricognizable character and a bunch of related error messages on the RStudio console, from Pango.
Problem is it is looking for a directory .../pango/1.6.0 that does not exist (I have /1.8.0).
Is there any one who came out with a working combination of R/RStudio/Rattle on Mavericks?
I have a course I'm going to teach on data mining next semester and I introduced Rattle as the core tool, but I need it running.
Going back to previous Mac OS is not an option, because students may have the latest version.
Any help would be highly appreciated
I believe that the problem is with the GTK2 and Cairo modules. After building a few packages from source, rattle works for me...
I have had difficulties with Cairo/GTK2 since Mountain Lion. I got crashes using Simon's binary packages for these. Note that I updated my system to Mavericks, so I have not tried this on a clean install... I also have Homebrew installed for building programs from source. I use the ATT binary installer for R (thanks, Simon) for most packages but build a few packages from source. There were some hiccups and I spent a lot of time searching with Google. Here is what I did:
One needs XCode and the Xcode command line tools installed. After you install XCode, you need to run
sudo xcode-select --install
to install the command line tools. Then install Homebrew according to directions from the web site... Install gtk+ and cairo with their dependencies with:
brew install gtk+ cairo
And wait quite a while for everything to build....
The first problem I had is that I couldn't build any R packages from source because of this error:
make: llvm-gcc-4.2: No such file or directory
Google to the rescue...
I needed to change two lines in Makeconf in /Library/Frameworks/R.framework/Resources/etc to
CC=clang
CXX=clang++
Note: the R Mac Tools page now says this should be:
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/clang4/bin/clang++
LDFLAGS=-L/usr/local/clang4/lib
Then download the source packages for RGtk2, Cairo, and cairoDevice. I do all the work in my ~/bld directory with:
cd ~/bld
export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/Library/Frameworks/GTK+.framework/Versions/Current/Resources/lib/pkgconfig:$PKG_CONFIG_PATH
R CMD install RGtk2_2.20.25.tar.gz
R CMD install Cairo_1.5-2.tar.gz
R CMD install cairoDevice_2.19.tar.gz
Hope this helps.
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.