I use a cluster (OS is Linux) which does not have R. I would like to install R in my personal folders so that I can just do
Rscript example.R arg1 arg2
How should I install R on this cluster knowing that I don't have admin rights?
How can I then manage the packages?
I'm not sure this is on-topic, but: all you really have to do is
download the R source tarball from CRAN; unpack it somewhere in your file space
create an r-build directory at the same level of the hierarchy (not technically necessary, but it's better practice to keep the source and build directories separate)
create an installation directory (say ~/r_install) somewhere sensible within your file space
cd to the source directory; tools/rsync-recommended
cd to the build directory
../[srcdir]/configure --prefix=~/r_install
make (to build the binaries)
make install (to move everything where it belongs; not technically necessary, as you can run R from the build directory)
Where this may get hairy is with all of the system requirements for R (LaTeX, Java, bzip2, etc. etc. ...) it is theoretically possible to download all this stuff and install it in your own file space, but it starts to get sufficiently tedious that it will be easier to beg your sysadmin to install at least the dependencies for you ...
as #Hack-R points out the basics of this answer are already present on Unix & Linux stackexchange, although my answer is a little more detailed ...
Related
When running the checks for my R-package (via devtools::check()) I face the warning ''qpdf' is needed for checks on size reduction of PDFs. I found this question were it was suggested (if I understood the answer correctly) to run Sys.which(Sys.getenv("R_QPDF", "qpdf")) and see whether qpdf is found or not. In my case this just returns
qpdf
""
so, I think I didn't install qpdf correctly. Unfortunately it seems to be quite complicated to install qpdf on Windows. My first side question is: does it really is so painful and complicated to install qpdf for Windows or is there an easy solution?
I've followed the instructions until it is said to add C:\MinGW-w64\bin and C:\MinGW-w64\lib\mingw to the PATH variable. But then I don't find further specific instructions to install qpdf, only about how to build qpdf with different other programs. The second side question is: is my assumption correct that after I've build qpdf it is installed? But the real question is: What is the best way to build qpdf? I tried the ./config-mingw32 and ./config-mingw64 commands from the section "Building with MinGW" in my C:\MinGW\msys\1.0\bin\bash.exe but got the error messages ./config-mingw32: No such file or directory and have no idea how to fix this issue.
I'm using Windows 10, R version 3.3.2 Patched (2017-01-07 r71934) -- "Sincere Pumpkin Patch" and RStudio 1.0.136.
You basically do not need to build the file on windows. Please follow three steps below:
Download qpdf for windows from https://sourceforge.net/projects/qpdf/?source=typ_redirect
Extract files in a temp folder
Copy the contents of the bin folder to %SystemRoot%\System32
job done!
Sys.which(Sys.getenv("R_QPDF", "qpdf"))
qpdf
"C:\\WINDOWS\\SYSTEM32\\qpdf.exe"
To flesh out an answer provided elsewhere:
If you are running the 32-bit version of R, it is important that you download the 32-bit version of qpdf, which is the version linked from the SourceForge homepage. If you are running a 64-bit installation of R, you will need to do a bit of digging to locate the 64-bit version of qpdf, which is buried a little more deeply (version 10.0.1 is listed here).
Rather than copying files to C:/Windows/System32, a potentially safer option is to extracted the zipped qpdf directory to C:\Program Files. If you do this, you'll need to add C:\Program Files\qpdf-version_number\bin to your system PATH under the environment variables.
To do this within R, run Sys.setenv('PATH' = paste0('C:\Program Files\qpdf-version_numer\bin;', Sys.getenv('PATH')))
To do this in Windows, open the start menu, type "edit the system environment variables" to open the System Properties, and at the bottom of the "Advanced" tab click "Environment variables". Find the "Path" entry under "System variables" and click "Edit". Then, re-start R so it picks up the modified PATH.
One further step may be required to convince Windows that pqdf is safe to run.
Navigate to C:\Program Files\qpdf-version_numer\bin and execute qpdf.exe (by double-clicking). Windows 10 throws up a security warning, as it's an unrecognized executable file. You'll need to use the more options link to find the button to run the program. This done, Windows will recognize the file as safe to run and allow other software, including R, to use it.
I'm trying to develop an R package that will include some previously compiled executable programs and their supporting libraries. (I know this is bad form, but it is for internal use).
My question: Does the special exec and tools directories have any special functionality within R?
The documentation seems to be sparse. Here is what I've figured out so far:
From here
files contained in exec are marked as executable on install
subdirectories in exec are ignored
exec is rarely used (my survey of CRAN says tools is just as rarely used)
tools is around for configuration purposes?
Do these directories offer any that I couldn't get from creating an inst/programs directory?
[R-exts] has this to say:
Subdirectory exec could contain additional executable scripts the
package needs, typically scripts for interpreters such as the shell,
Perl, or Tcl. This mechanism is currently used only by a very few
packages. NB: only files (and not directories) under exec are
installed (and those with names starting with a dot are ignored), and
they are all marked as executable (mode 755, moderated by ‘umask’) on
POSIX platforms. Note too that this is not suitable for executable
programs since some platforms (including Windows) support multiple
architectures using the same installed package directory.
It's quite possible the last note won't apply to you if it's only for internal use.
Nevertheless, I'd suggest avoiding abusing any existing convention that might not apply precisely to your situation, and instead use inst/tools or inst/bin.
As far as I can tell, here is the functionality offered by the exec and tools directories.
exec
From R-exts by way of hadley:
Subdirectory exec could contain additional executable scripts the package needs, typically scripts for interpreters such as the shell, Perl, or Tcl. This mechanism is currently used only by a very few packages. NB: only files (and not directories) under exec are installed (and those with names starting with a dot are ignored), and they are all marked as executable (mode 755, moderated by ‘umask’) on POSIX platforms. Note too that this is not suitable for executable programs since some platforms (including Windows) support multiple architectures using the same installed package directory.
exec features I have figured out
On POSIX platforms (*nix, os x), the files within exec will be marked as executable.
No subdirectories of exec are included in the package, only files in exec root
(note, it could contain binary executables, but there is no architecture/platform handling
tools
From R-exts:
Subdirectory tools is the preferred place for auxiliary files needed during configuration, and also for sources need to re-create scripts (e.g. M4 files for autoconf).
tools features I have figured out
tools is to hold files used at package compile time
All files contained are copied recursively into the source *.tar.gz package (including subdirs)
tools is not included in the final, compiled form of the package. All contents are dropped
I need to support an R environment on a Windows 7 PC that doesn't have internet access.
I'd like to download (to DVD, eventually) a current version of all ~ 5,000 packages to make available to users of R on this PC.
Is there an FTP script, or another good way, to download all of the zip files for the R packages?
I know there are daily updates to R, but one good day will be enough to get me started.
Presumably you have an installation somewhere that does have internet access. I would just set that installation to download everything. There's an example at http://www.r-bloggers.com/r-package-automated-download/. Start R, and try this:
pkg.list = available.packages()
download.packages(pkgs = pkg.list, destdir = "E:\MyRPackages")
Once you have these files, copy them to some kind of portable media (thumb drive, hard drive, whatever) or burn a CD / DVD and take that to the standalone machine.
Note: there may be a reason this other machine was not connected to the internet. So be careful! Make sure the virus protection is up to date on the non-connected machine, and that your IT folks won't come down on you like a ton of bricks for transferring data this way.
Next, you need to point the standalone machine at the portable media or the CD / DVD. A simple way to do this is to redefine where R looks for the repository. See e.g. Creating a local R package repository for examples.
In your case, try something like this in R:
update.packages(repos="complete-path-to-portable-media",repos = NULL, type = "source")
Use rsync to create a mirror and then install packages by pointing to your local mirror as the repos argument of install.packages. No need to make the repository publicly available. Specialize the path (e.g., to rsync based on /bin/windows/contrib/3.0/) to retrieve just the windows binaries (to a directory that you've created with similar structure repos/bin/windows/contrib/3.0/) if that's all that needs to be supported.
rsync -rtlzv --delete \
cran.r-project.org::CRAN/bin/windows/contrib/3.0/ \
repos/bin/windows/contrib/3.0/
I have accession to universities server: Red Hat Enterprise Linux release 6.2.
My work is to test various scientific analysis programs.
I have no problem untar'ing and running them in my local directory. But most of them have lots of dependencies (perl libraries, RE2, GNU SL, glibc.i686 ) - whenever I try to install those dependencies I come up with the permission problem.
All of those packages require root to install.
Is there a way how can I install various different packages only in my local directory without asking root to install them system wide?
Yes, but the procedure varies per package. Many modern Unix packages have a configure script that you must run, which takes a --prefix option + argument specifying where the package should be installed. A directory such as $HOME/pkg would be a good options for these. Other configuration/building/installation scripts have similar options.
When building a package with dependencies, make sure you have $HOME/pkg/bin in your PATH, $HOME/pkg/lib in your LD_LIBRARY_PATH and pass -I$HOME/pkg/include and -L$HOME/pkg/lib to the compiler and linker, respectively. E.g., put the following in your shell startup file (.bashrc for Bash):
PATH=$HOME/pkg/bin:$PATH
CFLAGS=-I$HOME/pkg/include
LDFLAGS=-L$HOME/pkg/lib
LD_LIBRARY_PATH=$HOME/pkg/lib
(You shouldn't have to install glibc, ever.)
Question: How do I move all of the most up-to-date R packages into one simple location that R (and everything else) will use from now and forever for my packages?
I have been playing around with R on Ubuntu 10.04 using variously RGedit, RCmdr, R shell, and RStudio. Meanwhile, I have installed packages, updated packages, and re-updated packages via apt, synaptic, install.packages(), etc... which apparently means these packages get placed everywhere, and (with the occasional sudo tossed in) with different permissions.
Currently I have different versions of different (and repeated) packages in:
/home/me/R/i486-pc-linux-gnu-library/2.10
/home/me/R/i486-pc-linux-gnu-library/2.14
/home/me/R/i486-pc-linux-gnu-library/
/usr/local/lib/R/site-library
/usr/lib/R/site-library
/usr/lib/R/library
First - I'm a single user, on a single machine - I don't want multiple library locations, I just want it to work.
Second - I am on an extremely slow connection, and can't keep just downloading packages repeatedly.
So - is there an easy way to merge all these library locations into one simple location? Can I just copy the folders over?
How do I set it in concrete that this is and always will be where anything R related looks for and updates packages?
This is maddening.
Thanks for your help.
Yes, it should almost work to just copy the folders over. But pre-2.14 packages WITHOUT a NAMESPACE file probably won't work in R 2.14 where all packages must have a namespace...
And you'd want to manually ensure you only copy the latest version of each package if you have multiple versions...
If you type .libPaths(), it will tell you where R looks for packages. The first in the list is where new packages are typically installed. I suspect that .libPaths() might return different things from RStudio vs. Rcmd etc.
After piecing together various bits of info here goes: A complete moron's guide to the R packages directory organization:
NB1 - this is my experience with Ubuntu - your mileage may vary
NB2 - I'm a single user on a single machine, and I like things simple.
Ubuntu puts anything installed via apt, or synaptic in:
/usr/lib/R/site-library
/usr/lib/R/library
directories. The default vanilla R install will try install packages here:
/usr/local/lib/R/site-library
Since these are system directories the user does not have write privileges to, depending on what method you are interacting with R you might be prompted with a friendly - "Hey buddy - we can't write there, you want us to put your packages in your home directory?" which seems innocent and reasonable enough... assuming you never change your GUI, or your working environment. If you do, the new GUI / environment might not be looking in the directory where the packages were placed, so won't find them. (Most interfaces have a way for you to point where your personal library of packages is, but who wants to muck about in config files?)
What seems to be the best practice for me (and feel free to correct me if I'm wrong) with a default install setup on Ubuntu, is to do any package management from a basic R shell as sudo: > sudo R and from there do your install.packages() voodoo. This seems to put packages in the usr/local/lib/R/site-library directory.
At the same time, update.packages() will update the files in /usr/lib/R/site-library and usr/lib/R/library directories, as well as usr/local/lib/R/site-library
(As for usr/lib/R/ division, it looks like /library/ has the core packages, while /site-library/ holds anything added, assuming they were installed by apt...)
Any packages previously installed and in the wrong place can be moved to the /usr/local/lib/R/site-library directory (assuming you are sudoing it) just by moving the directories (thanks #Tommy), but as usr/lib/R/ is controlled by apt - best not add or subtract anything from there...
Whew. Anyway - simple enough, and in simple language. Thanks everyone for the help.