Related
I am working on a remote server using RStudio. This server has no access to the Internet. I would like to install the package "stringi." I have looked at this stackoverflow article, but whenever I use the command
install.packages("stringi_0.5-5.tar.gz",
configure.vars="ICUDT_DIR=/my/directory/for/icudt.zip")
It simply tries to access the Internet, which it cannot do. Up until now I have been using Tools -> Install Packages -> Install from Packaged Archive File. However, due to this error, I can no longer use this method.
How can I install this package?
If you have no internet access on local machines, you can build a distributable source package that includes all the required
ICU data files (for off-line use) by omitting some relevant lines in
the .Rbuildignore file. The following command sequence should do the trick:
wget https://github.com/gagolews/stringi/archive/master.zip -O stringi.zip
unzip stringi.zip
sed -i '/\/icu..\/data/d' stringi-master/.Rbuildignore
R CMD build stringi-master
Assuming the most recent development version is 1.3.1,
a file named stringi_1.3.1.tar.gz is created in the current working directory.
The package can now be installed (the source bundle may be propagated via
scp etc.) by executing:
R CMD INSTALL stringi_1.3.1.tar.gz
or by calling install.packages("stringi_1.3.1.tar.gz", repos=NULL),
from within an R session.
For a Linux machine the easiest way is from my point of view:
Download the release you need from Rexamine in tar.gz format to your local pc. In opposition to the version on CRAN it already contains the icu55\data\ folder.
Move the archive to your target linux machine without internet access
run R CMD INSTALL stringi-1.0-1.tar.gz (in case of release 1.0-1)
You provided the wrong value of configure.vars.
It indicates that you have to give the directory's name, not a final file name.
Correct your code to the following:
install.packages("stringi_0.5-5.tar.gz",
configure.vars="ICUDT_DIR=/my/directory/for/")
Regards,
Sean
Follow the steps below
Download icudt55l.zip seperately from server where you have internet access with
wget http://www.mini.pw.edu.pl/~gagolews/stringi/icudt55l.zip
Copy the downloaded packages to the server where you want to install stringi
Execute the following command
R CMD INSTALL --configure-vars='ICUDT_DIR=/tmp/ALL' stringi_1.1.6.tar.gz
icudt55l.zip is copied to /tmp/ALL
The suggestion from #gagolews almost worked for me. Here's what actually did the trick with RStudio.
Download the master.zip file that will save as stringi-master.zip.
Unzip the file onto your desktop. The unzipped folder should be stringi-master.
Edit the .Rbuildignore file by removing ^src/icu55/data and ^src/icu61/data or similar lines.
Move the folder from your desktop to the home directory of your server.
Create a New Project in RStudio with ~/stringi-master as the Existing Directory
From RStudio's menu, select Build and Build Source Package. (You may need to first select Configure Build Tools. For Project build tools choose Package then select OK.)
It should create a tar.gz file, in the following format: stringi_x.x.(x+1).tar.gz. For example, if the current version of stringi is 1.5.3, it will create version 1.5.4. (I received a few warnings that didn't seem to affect the outcome.)
Move the newly created package to your local repository. Update the repository index. And install the package.
I am using R 2.13.0 with windows 7, after giving my user full privileges to the R folder (as described here).
This allows me to install new packages just fine.
However, when using update.packages(), to update existing packages, I keep getting the following error (for example, when updating the MASS package):
package 'MASS' successfully unpacked and MD5 sums checked
Warning: unable to move temporary installation
'C:\Program
Files\R\R-2.13.0\library\file6cae3bcf\MASS'
to 'C:\Program
Files\R\R-2.13.0\library\MASS'
Any suggestions on how to fix this?
p.s: Running R as an administrator or shifting the library location out of Program Files is not a solution (it's a hack - but I am looking for a solution)
I found that the problem indeed is the antivirus "real time file system protection". I do the following to fix the problem:
trace(utils:::unpackPkgZip, edit=TRUE)
I edit line 140 (line 142 in R 3.4.4):
Sys.sleep(0.5)
to:
Sys.sleep(2)
I seems like the antivirus stalls the creation of the package tmp dir. After changing it to 2 seconds the error is gone.
EDIT: to do this programmatically execute
trace(utils:::unpackPkgZip, quote(Sys.sleep(2)), at = which(grepl("Sys.sleep", body(utils:::unpackPkgZip), fixed = TRUE)))
(credits #DavidArenburg)
Just to update everyone, I (think that I) found out the source of the problem: antivirus.
The "real time file system protection" was blocking R from copying the files between folders once they were downloaded.
Upon adding the R directory to the exception list (coupled with adding user permission and installing R on D:\R), and the problem went away. With all of this work, I might as well switch to Linux (I should, really...)
(I updated my post with the above information: http://www.r-statistics.com/2011/04/how-to-upgrade-r-on-windows-7/)
I hope it will help someone in the future,
Tal
If you cannot turn off your antivirus, due to corporate policy for example, here is a workaround that I found. Debugging the unzip package function and then stepping through it gives the antivirus enough time to do its job without interfering. Use this command:
debug(utils:::unpackPkgZip)
install.packages("packageName")
and then step through the code (by pressing enter many times) when R starts debugging during the installation.
I found this solution here.
If you can just download the binary straight from CRAN. On windows when downloaded it will be a zip file. Now manually unzip this into the ..library/ folder of your R (.libPaths()). It worked for me on some packages.
I had this problem installing both swirl and dplyr. I am working on Windows 64-bit.
Warning: unable to move temporary installation
What I did is I accessed my temporary files on the C: drive, and opened my file extractor program and I extracted the files from the temp file in the C: drive to my R program files in the C: drive, by manually copying them. THIS WORKED FOR BOTH dpylr and swirl. Stoked!
Cheers,
Peach
Can you not use the lib.loc parameter to only update packages in your personal library (in user)?
There should be no way to enable a normal, non-augmented user to change files in the program files folder, so the only thing you can do (if you don't want to augment the user) is to have R not updating packages there.
A workaround is to avoid installing R in the program files folder (which may be more or less of a hack than just shifting the library location out of it, depending on your point of view).
Finally, if lib.loc doesn't cut it, you can look at the source code for update.packages and create your own customized version that will always avoid the common library location in program files.
I just met the same question, and the solution I found out was that you should install packages using the original R software (plus, you should choose the right mirror site, some of them are blocked). At first I used Rstudio to install packages and I got the same problem as you met. Hope this is helpful.
I have run into this error several times. In my own case, it is because our admins want us to use remote virtual disks (on Windows 7) for our files and everything is locked up tight as a drum. The only way I can use R packages is in a lib directory on that remote virtual disk. This wouldn't be a problem except that the network isn't always smooth and fast. Thus, when I need a package, especially one with several other packages in tow (e.g., MBESS), I either have to go through the get.packages() process multiple times until it finally finishes or make it IT's headache to do quick like the bunny for me. I can't always wait for IT.
I just went to the library folder (Windows XP) and deleted all fileXXXX folders. Reran the install an it is worked.
I had the same problem. Since the issue seems to be the antivirus blocking the transf of a downloaded file, I tried a different download method in the install.packages and it worked.
For example:
install.packages("stringr", method = "curl")
You must go into the properties of the R folder and change the security parameters. You can enable the option to write and modify for all users.
The error : "unable to move temporary installation" is basically arising due to any of the antivirus running on your system.
Try unzipping the downloaded file from the Temp folder into the default library path (you can get it by running .libPaths() in R session).
I'm using a MRAN and I was having so many versioning issues. Trying to work with tidyverse and ggplot2 and by upgrading to the latest version from Microsoft it solved all of my R-Studio versioning issues.
Version info:
Microsoft R Open 3.5.1
The enhanced R distribution from Microsoft
Default CRAN mirror snapshot taken on 2018-08-01.
Download Microsoft R Open 3.5.1
Normally I install packages using:
install.packages("foo")
and a Repo over the internet. But I have a new machine now where I want to replicate the packages from my existing installation without having to pull everything off the internet all over again. (I've a ton of packages and slow internet access)
Both machines are Windows and run the same R version. (2.13.1)
Is there a way to do this? Closest I can get is I know I can install from local zip files using:
install.packages("pathtozip", repos = NULL)
But does R store all Zips somewhere? I found a few in locations like:
C:\Documents and Settings\foouser\Local Settings\Temp\RtmpjNKkyp\downloaded_packages
But not all.
Any tips?
The function .libPaths will give you a vector of all the libraries on your machine. Run this on your old machine to find all of them. You can simply copy all these files into the libraries on your new machine (run .libPaths on it too to find out where).
Alternatively, if you want to set up a real repository (i.e. basically a CRAN mirror) on your computer or on a network drive you can update, you can put binary or source packages into a folder and run tools::write_PACKAGES on that folder. You can them run install.packages using the contriburl argument and point it to your repository folder.
All packages that you have installed are stored in a folder called win-library\r-version, for example,
C:\Users\Ehsan\Documents\R\win-library\2.15 so, it is enough to copy all the folders inside 2.15 to the same folder in your new machine. because you have the same version of R you do not need to update them by update.packages().
On your original computer, run
write.csv(unique(data.frame(installed.packages())[,1]),"packages.csv",row.names=F)
Save this .csv into the working directory of your new computer, then run
install.packages(as.character(read.csv("packages.csv")[,1]))
You can check what your working directory is using getwd().
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.
I am using R 2.13.0 with windows 7, after giving my user full privileges to the R folder (as described here).
This allows me to install new packages just fine.
However, when using update.packages(), to update existing packages, I keep getting the following error (for example, when updating the MASS package):
package 'MASS' successfully unpacked and MD5 sums checked
Warning: unable to move temporary installation
'C:\Program
Files\R\R-2.13.0\library\file6cae3bcf\MASS'
to 'C:\Program
Files\R\R-2.13.0\library\MASS'
Any suggestions on how to fix this?
p.s: Running R as an administrator or shifting the library location out of Program Files is not a solution (it's a hack - but I am looking for a solution)
I found that the problem indeed is the antivirus "real time file system protection". I do the following to fix the problem:
trace(utils:::unpackPkgZip, edit=TRUE)
I edit line 140 (line 142 in R 3.4.4):
Sys.sleep(0.5)
to:
Sys.sleep(2)
I seems like the antivirus stalls the creation of the package tmp dir. After changing it to 2 seconds the error is gone.
EDIT: to do this programmatically execute
trace(utils:::unpackPkgZip, quote(Sys.sleep(2)), at = which(grepl("Sys.sleep", body(utils:::unpackPkgZip), fixed = TRUE)))
(credits #DavidArenburg)
Just to update everyone, I (think that I) found out the source of the problem: antivirus.
The "real time file system protection" was blocking R from copying the files between folders once they were downloaded.
Upon adding the R directory to the exception list (coupled with adding user permission and installing R on D:\R), and the problem went away. With all of this work, I might as well switch to Linux (I should, really...)
(I updated my post with the above information: http://www.r-statistics.com/2011/04/how-to-upgrade-r-on-windows-7/)
I hope it will help someone in the future,
Tal
If you cannot turn off your antivirus, due to corporate policy for example, here is a workaround that I found. Debugging the unzip package function and then stepping through it gives the antivirus enough time to do its job without interfering. Use this command:
debug(utils:::unpackPkgZip)
install.packages("packageName")
and then step through the code (by pressing enter many times) when R starts debugging during the installation.
I found this solution here.
If you can just download the binary straight from CRAN. On windows when downloaded it will be a zip file. Now manually unzip this into the ..library/ folder of your R (.libPaths()). It worked for me on some packages.
I had this problem installing both swirl and dplyr. I am working on Windows 64-bit.
Warning: unable to move temporary installation
What I did is I accessed my temporary files on the C: drive, and opened my file extractor program and I extracted the files from the temp file in the C: drive to my R program files in the C: drive, by manually copying them. THIS WORKED FOR BOTH dpylr and swirl. Stoked!
Cheers,
Peach
Can you not use the lib.loc parameter to only update packages in your personal library (in user)?
There should be no way to enable a normal, non-augmented user to change files in the program files folder, so the only thing you can do (if you don't want to augment the user) is to have R not updating packages there.
A workaround is to avoid installing R in the program files folder (which may be more or less of a hack than just shifting the library location out of it, depending on your point of view).
Finally, if lib.loc doesn't cut it, you can look at the source code for update.packages and create your own customized version that will always avoid the common library location in program files.
I just met the same question, and the solution I found out was that you should install packages using the original R software (plus, you should choose the right mirror site, some of them are blocked). At first I used Rstudio to install packages and I got the same problem as you met. Hope this is helpful.
I have run into this error several times. In my own case, it is because our admins want us to use remote virtual disks (on Windows 7) for our files and everything is locked up tight as a drum. The only way I can use R packages is in a lib directory on that remote virtual disk. This wouldn't be a problem except that the network isn't always smooth and fast. Thus, when I need a package, especially one with several other packages in tow (e.g., MBESS), I either have to go through the get.packages() process multiple times until it finally finishes or make it IT's headache to do quick like the bunny for me. I can't always wait for IT.
I just went to the library folder (Windows XP) and deleted all fileXXXX folders. Reran the install an it is worked.
I had the same problem. Since the issue seems to be the antivirus blocking the transf of a downloaded file, I tried a different download method in the install.packages and it worked.
For example:
install.packages("stringr", method = "curl")
You must go into the properties of the R folder and change the security parameters. You can enable the option to write and modify for all users.
The error : "unable to move temporary installation" is basically arising due to any of the antivirus running on your system.
Try unzipping the downloaded file from the Temp folder into the default library path (you can get it by running .libPaths() in R session).
I'm using a MRAN and I was having so many versioning issues. Trying to work with tidyverse and ggplot2 and by upgrading to the latest version from Microsoft it solved all of my R-Studio versioning issues.
Version info:
Microsoft R Open 3.5.1
The enhanced R distribution from Microsoft
Default CRAN mirror snapshot taken on 2018-08-01.
Download Microsoft R Open 3.5.1