I'm an undergraduate research assistant working on a Linux server without root privilege. I'm trying to install the Rstudio server but the Rstudio website only provides the installation method for sudoers. Is it possible to install it without root access? I'm asking because I'm really not sure if I could get access from the manager. Any help will be appreciated!
No, you can't install it without root access. But there are a couple of things you could do to piece together a solution. Here are two options:
Extract the server and run it directly
You have to be root to install packages, so you can't install the .deb/.rpm file yourself. However, you could extract the contents of the file to a directory inside your home directory and run RStudio Server from there, by executing the rserver program in a regular shell.
Note that this will probably require an afternoon of editing the rserver.conf file to tell it where to find the rest of the files in the installation (since it presumes they are installed in /usr/lib by default). You can get some inspiration for how to do this here: https://github.com/rstudio/rstudio/blob/master/src/cpp/conf/rserver-dev.conf
Run the desktop version and forward the graphics
The other route is to run RStudio Desktop on the server; we make several builds of RStudio Desktop that are installer-less and can just be unpacked into your home directory. Then run an X11 server on your own computer and an X11 client on the RStudio server, so that the RStudio Desktop instance appears on your computer instead of the server.
Yes, you can run rserver without root priveliges.
For RStudio 1.4 I patched the following line into src/cpp/core/LogOptions.cpp
const FilePath kDefaultLogPath = core::system::xdg::userDataDir().completePath("log");
Then you need to set the system environment variables to some location read-writeable for the user, like
RSTUDIO_CONFIG_DIR=$HOME/.config/rstudio
RSTUDIO_CONFIG_HOME=$HOME/.config/rstudio
RSTUDIO_DATA_HOME=$HOME/.local/share/rstudio
And start rserver with the option
--server-data-dir={directory writeable for user}
--server-pid-file={file-path creatable for user}
--database-config-file={config-file}
With these adjustments it runs for me when I start it as a simple user (no root privileges) with
rserver --auth-none=1 --www-frame-origin=same --www-port={port} --www-verify-user-agent=0 --server-data-dir={my-tmp-path} --server-pid-file={my-tmp-path}/rstudio.pid --database-config-file={my-tmp-path}/db.conf}
ATTENTION:
But be aware, that anyone who can reach your system and the specified port from the network has access to the running RStudio in his browser and therefore can run any command in the name of the user on your system now.
I am trying to install some R packages on my account on the HPC cluster. However when I do that I get the following error:
no permission to install to directory '/gpfs1/apps/sw/R/R-3.6.1/lib64/R/library'
I have contacted the admin and he told me I do need admin privilages to install anything to /gpfs1/apps/sw/. He told I must rather do that in the home directory.
How can I switch to the home directory on my account ? The admin has already installed some other R packages on my account but I need to install some myself ? How do I know where my R packages are on the home directory and how to install everything there ?
Output of .libPaths()
"/gpfs1/apps/sw/R/R-3.6.1/lib64/R/library"
Update
Using the following tutorial I am now able to install R packages in my home directory on the cluster using the following command:
export R_LIBS_USER=/home/rcf-proj/tt/trojan/R/parallel:$R_LIBS_USER
which adds the path above to .libPaths(). However, when running my R script it keeps referring to the original location /gpfs1/apps/sw/R/R-3.6.1/lib64/R/library where I don't have the packages I installed in my HOME directory. Especially that after I restart R, I must always do this command.
In the answers here They recommended I edit the .libPaths() in the .Rprofile file, but I cannot seem to find it on my cluster account. The same issue is still open here
I have read it somewhere that we car create a .Rprofile ourselves, but how can I do this and what must I put in it ??
I have had to install Ubuntu command line on windows10 in order to install R and download a package that is not supported on R for windows. This has worked fine, however, I need to set the working directory in R to the folder containing the files the package needs to work with. I have looked at lots of forums about changing directory and I have no luck!
My default working directory is a hidden folder created by windows when I installed ubuntu command line. I can access this, but I dont need this folder...I need to change the working directory in R to a folder on the D drive on my computer. I have tried to no avail!!
I have tried the normal setwd() command with the following combinations, all of which return the error 'cannot change working directory'
setwd("D:/RNA-seq data/")
setwd("d:/RNA-seq)
setwd("~D:/RNA-seq)
I am really frustrated that I cannot carry out this simple command (maybeI am doing something fundamentally wrong) or maybe this is a limitation because of the hidden default home folder set by windows? Please not I cannot transfer the necessary files in to the default folder created by windows for 'home/R' as it is on the C drive and there isnt enough space on disk. I need to navigate to the folder on d drive in order to carry out my code!!
Any help would be really really appreciated! Many thanks!
I was wondering why it won't let me change my working directory.
I keep seeing this error:
Error in setwd(dataDir) : cannot change working directory
This is my code:
dataDir <- "C:/Documents and Settings/My Documents/R/"
setwd(dataDir)
Seems to be an annoying Windows permissions issue; that's a legacy directory.
There are 2.93 million Google hits along the lines of "Windows (7/)10: Access to the path 'C:\Documents and Settings' is denied". Look for advice in Windows forums, and check what the ownership and permissions on "C:/Documents and Settings/My Documents/..." are currently, and what they're supposed to be, and whether Administrator account is enabled. (Frankly not the best choice for the R install packages directory, but many installers use it, or default to it.)
Please confirm that setwd() works fine for a more harmless choice of directory, e.g. 'C:\Users\your_name\R'
Are you running R as Administrator or User?
Did you install R as Administrator or User? (which installer did you use, and which installer version/date? R-project's? Anaconda? another?)
There must be an error in the path. It should look like C:\<your_username>\Documents and Settings\My Documents
Or try
setwd("C:\\[your_username]\\Documents and Settings\\My Documents\\R")
"Documents and Settings" is a directory that exists in really old versions of Windows (XP and earlier). In Windows 10, your user data is under C:\users\<username>, and your documents are in C:\users\<username>\Documents.
As far as R is concerned, under Windows 10 the home directory ~ maps to C:\users\<username>\Documents.
Run Rstudio as Admin.
then run dataDir <- "C:/Documents and Settings/My Documents/R/"
setwd(dataDirstrong text**)**
I have attempted to install R and R studio on the local drive on my work computer as opposed to the organization network folder because anything that runs through the network is really slow. When installing, the destination path shows that it's my local C:drive. However, when I install a new package, the default path shown is my network drive and there is no option to change:
.libPaths()
[1] "\\\\The library/path/I/don't/want"
[2] "C:/Program Files/R/R-3.2.1/library"
I'm running windows 7 professional. How can I remove library path [1] and make path [2] my primary for all base packages and all new packages that I install?
Windows 7/10: If your C:\Program Files (or wherever R is installed) is blocked for writing, as mine is, then you'll get frustrated editing RProfile.site (as I did). As specified in the accepted answer, I updated R_LIBS_USER and it worked. However, even after reading the fine manual several times and extensive searching, it took me several hours to do this. In the spirit of saving someone else time...
Let's assume you want your packages to reside in C:\R\Library:
Create the folder C:\R\Library. Next I need to add this folder to the R_LIBS_USER path:
Click Start --> Control Panel --> User Accounts --> Change my environmental variables
The Environmental Variables window pops up. If you see R_LIBS_USER, highlight it and click Edit. Otherwise click New. Both actions open a window with fields for Variable and Value.
In my case, R_LIBS_USER was already there, and Value was a path to my desktop. I added to the path the folder that I created, separated by semicolon. C:\R\Library;C:\Users\Eric.Krantz\Desktop\R stuff\Packages.
(NOTE: In the last step, I could have removed the path to the Desktop location and simply left C:\R\Library).
See help(Startup) and help(.libPaths) as you have several possibilities where this may have gotten set. Among them are
setting R_LIBS_USER
assigning .libPaths() in .Rprofile or Rprofile.site
and more.
In this particular case you need to go backwards and unset whereever \\\\The library/path/I/don't/want is set.
To otherwise ignore it you need to override it use explicitly i.e. via
library("somePackage", lib.loc=.libPaths()[-1])
when loading a package.
Facing the very same problem (avoiding the default path in a network) I came up to this solution with the hints given in other answers.
The solution is editing the Rprofile file to overwrite the variable R_LIBS_USER which by default points to the home directory.
Here the steps:
Create the target destination folder for the libraries, e.g.,
~\target.
Find the Rprofile file. In my case it was at C:\Program Files\R\R-3.3.3\library\base\R\Rprofile.
Edit the file and change the definition the variable R_LIBS_USER. In my case, I replaced the this line file.path(Sys.getenv("R_USER"), "R", with file.path("~\target", "R",.
The documentation that support this solution is here
Original file with:
if(!nzchar(Sys.getenv("R_LIBS_USER")))
Sys.setenv(R_LIBS_USER=
file.path(Sys.getenv("R_USER"), "R",
"win-library",
paste(R.version$major,
sub("\\..*$", "", R.version$minor),
sep=".")
))
Modified file:
if(!nzchar(Sys.getenv("R_LIBS_USER")))
Sys.setenv(R_LIBS_USER=
file.path("~\target", "R",
"win-library",
paste(R.version$major,
sub("\\..*$", "", R.version$minor),
sep=".")
))
Windows 10 on a Network
Having your packages stored on the network drive can slow down the performance of R / R Studio considerably, and you spend a lot of time waiting for the libraries to load/install, due to the bottlenecks of having to retrieve and push data over the server back to your local host. See the following for instructions on how to create an .RProfile on your local machine:
Create a directory called C:\Users\xxxxxx\Documents\R\3.4 (or whatever R version you are using, and where you will store your local R packages- your directory location may be different than mine)
On R Console, type Sys.getenv("HOME") to get your home directory (this is where your .RProfile will be stored and R will always check there for packages- and this is on the network if packages are stored there)
Create a file called .Rprofile and place it in :\YOUR\HOME\DIRECTORY\ON_NETWORK (the directory you get after typing Sys.getenv("HOME") in R Console)
File contents of .Rprofile should be like this:
#search 2 places for packages- install new packages to first directory- load built-in packages from the second (this is from your base R package- will be different for some)
.libPaths(c("C:\Users\xxxxxx\Documents\R\3.4", "C:/Program Files/Microsoft/R Client/R_SERVER/library"))
message("*** Setting libPath to local hard drive ***")
#insert a sleep command at line 12 of the unpackPkgZip function. So, just after the package is unzipped.
trace(utils:::unpackPkgZip, quote(Sys.sleep(2)), at=12L, print=TRUE)
message("*** Add 2 second delay when installing packages, to accommodate virus scanner for R 3.4 (fixed in R 3.5+)***")
# fix problem with tcltk for sqldf package: https://github.com/ggrothendieck/sqldf#problem-involvling-tcltk
options(gsubfn.engine = "R")
message("*** Successfully loaded .Rprofile ***")
Restart R Studio and verify that you see that the messages above are displayed.
Now you can enjoy faster performance of your application on local host, vs. storing the packages on the network and slowing everything down.
I was struggling for a while with this as my work computer (with Windows 10) created the default user library on a network drive, which would slow down R and RStudio to an unusable state.
In case this helps someone, this is the easiest way I found, without requiring admin rights:
make sure the directory you want to install your packages into exists. If you want to respect the convention, use: C:\Users\username\R\win-library\rversion (for example, something like: C:\Users\janebloggs\R\win-library\3.6)
create a .Renviron file in your home directory (which might be on the network drive?), and in it, write one single line that defines the R_LIBS_USER variable to be your custom path:
R_LIBS_USER=C:\Users\janebloggs\R\win-library\3.6
(feel free to add comments too, with lines starting with #)
If a .Renviron file exists, R will read it at startup and use the variables as they are defined in there, before running the code in the .Rprofile. You can read about it in help(Startup).
Now it should be persistent between sessions!
After a couple of hours of trying to solve the issue in several ways, some of which are described here, for me (on Win 10) the option of creating a Renviron file worked, but a little different from what was written here above.
The task is to change the value of the variable R_LIBS_USER. To do this two steps needed:
Create the file named Renviron (without dot) in the folder \Program\etc\ (Program is the directory where R is installed--for example, for me it was C:\Program Files\R\R-4.0.0\etc)
Insert a line in Renviron with new path: R_LIBS_USER = "C:/R/Library"
After that, reboot R and use .libPaths() to confirm the default directory changed.
I think I tried all of the above and it didn't work for me. This worked, though:
In home directory, make a file called ".Renviron"
In that file, write:
.libPaths(new = "/my/path/to/libs")
Save and restart R if you had it open