I was unable to install a R package through GUI R.app on macOS, using a package installer GUI. In the past, I was able to install it without any problems.
The problem is when I tried to install a package, an error Currently it is not possible to install binary packages from a remote repository as root. occurred. I might not be good at the system-level knowledge, so want to use GUI as I have used it. But what is preventing the GUI from working any longer? Maybe from Yosemite it is no longer working?
And finally, is it still possible to use GUI package installer in this situation?
UPDATE
Hmmm... It seems that after updating to 3.3.1 (I used 3.3), the problem has gone away. I can install packages both at User Level and System Level without any problems. I don't know why, but someone can clarify it in case I would face the same problem in the future?
Related
I have just updated to R4.2.0 (previously R3.2) and I now get R Session Aborted when loading the package on windows. Same error when running directly from R. Everything seems ok when I install the mailR package. I also updated all dependencies.
Could someone help with this?
I had to update my RTools to the newest version, 4.2
https://cran.rstudio.com/bin/windows/Rtools/rtools42/rtools.html
Then I uninstalled both rJava and mailR, and reinstalled them again after the update without any issue.
Just as a side note, after a lot of headaches in Linux with mailR, trying to keep my java libraries updated, I finally switched to a curl-based email library, emayili: https://datawookie.github.io/emayili/
I found those Java dependencies would crop up as issues a few times a year in different systems, and haven't had any of the same with the new libraries.
after updating my R version to 3.6.1 version - the rGrain and rGraphviz packages do not work. First the error was suggesting that the packages are not writable. However after updating some libraries and trying to source it outside from the BiocManager right now the error appears saying that the compilation fails. Does anybody know how to fix it?
I have already tried multiple options like sourcing it outside and directly from BiocManager and other sources however with no results.
I would appreciate any type of help suggesting how to fix or just install packages gRain and Rgraphviz.
Not writable is biocmanager being poorly programmed and somehow wanting to install some secondary packages into the main R folder in program files, rather than the usual R\win-library\ in documents.
You can workaround that by launching the R console or Studio with administrator privileges when installing/updating.
I asked a similar question a couple months ago, but the package, website, and code in question have since been updated and the solution I used previously is no longer effective.
The issue is that I am unable to install a particular package in R.
The new code provided for installation of the DeclareDesign package is as follows (source):
install.packages("devtools")
devtools::install_github("DeclareDesign/DeclareDesign")
I've provided a screenshot of the error that I get when I try to run the above code. It looks to me like the problem is with the included 'estimatr' package, which apparently then causes the entire installation to fail.
How do I get this to work?
Your installation failed because devtools is trying to install estimatr from source, but you don't have the appropriate toolchain available to build it.
DeclareDesign now has a drat repository with pre-built binary packages for Mac and Windows, which should obviate the need to install Xcode or Rtools.
install.packages("DeclareDesign", repos="http://r.declaredesign.org")
DeclareDesign is now on CRAN, so you can install via
install.packages("DeclareDesign")
I am trying to install R on a RedHat server with no connectivity to the Internet. (sigh)
Initially, I tried with R meta package from EPEL (http://fedoraproject.org/wiki/EPEL).
Due to dependency requirements, I downloaded dependancies Rcore ,libRmath, etc...
Each time it prompts for a dependency, I download, transfer and install.
This takes time and manual effort.
Is there a cleaner way to do this than the manual download, transfer and install of every single dependency?
Note: The server has no internet connection, so yam is not helpful.
Have you thought of simply compiling R from source?
I usually do that, and it is relatively painless.
The thing is that when you do the ./configure step
you should get a list of all librarires that you
need before you issue make.
It might be less of a hazzle than the redhat install
you are doing.
I believed we are unable install R without online (unless there was someone download the installer and pass to you). You can refer to Setup ®Studio Server (CentOS/RHEL 7). Hope this helps.
One thing you could do is install R on a server with internet access.
Install Rtools.
Then you install all the packages you need with the option destdir of install.packages.
You will then get a folder with all the packages you will need.
My Fedora system (Fedora 20, all up to date) has just had R updated to version 3.1.0. Since then, I've had issues installing multiple packages. glmnet failed previously, and now I'm having trouble with treemap. More specifically, I get an error during treemap installation that httpuv has zero exit status.
I never had issues with the previous version of R. Any reason this version should have such problems??
There could be many causes to do with your OS, version, permissions, other installed packages/software, etc, etc. Without seeing the full error message it's hard to know.
One possibility specific to httpuv is root privileges. I've noticed a few threads on various forums when searching for installation errors with this package and Linux, many of them mentioning root v. non-root issues. In another case, libuv needed to be upgraded.
I encounter package installation problems daily and I have some more general work-arounds as well. Hopefully one of these will solve your problem.
Install the package from source
download.file(url="http://cran.r-project.org/src/contrib/httpuv_1.3.0.tar.gz", destfile = "httpuv.tar.gz")
install.packages("httpuv.tar.gz", type = "source", repos = NULL)
Install using devtools via GitHub if the package supports it
Install RTools and re-try your package installation
Install an older version of the package
If those above do not work, then I dig deeper by referring to advice given to me by a VP of IT in my company. These comments were made in reference to frequent package installation problems I encountered when switching from Windows to Solaris:
There are two types of install/make problems. Missing .h files
and/or missing .so/.a libs. The reason for these are multiple:
1.- the package that delivers these is not installed. This means that those files cannot be found anywhere in the /usr tree. Solution is
install right package, make sure the files are there
2.- the includes are not found by the install configurator. This means some environment variable or install option is not properly set (this
is our case for RODBC). Figuring out which variable to set is
challenging without looking at the package documentation [fortunately, documentation is not hard to find!]
3.- the libs are not in the LD_LIBRARY_PATH, easy to fix.
4.- There is a deeper compile/link error, meaning the package is not compatible with the rest of the sw, or has not been properly ported.