While trying to install a package inside RStudio on macOS Catalatina, it fails with a Permission Denied error:
> install.packages("mlbench")
trying URL 'https://cran.rstudio.com/src/contrib/mlbench_2.1-1.tar.gz'
Content type 'application/x-gzip' length 920768 bytes (899 KB)
==================================================
downloaded 899 KB
* installing *source* package ‘mlbench’ ...
** package ‘mlbench’ successfully unpacked and MD5 sums checked
mv: rename /usr/local/Cellar/r/3.6.1_1/lib/R/library/mlbench to /usr/local/Cellar/r/3.6.1_1/lib/R/library/00LOCK-mlbench/mlbench: Permission denied
ERROR: cannot remove earlier installation, is it in use?
* removing ‘/usr/local/Cellar/r/3.6.1_1/lib/R/library/mlbench’
Warning in install.packages :
installation of package ‘mlbench’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/bc/wsz930gj3gn5zgq4hbm6jkfr0000gn/T/RtmpdvQLox/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning in install.packages :
cannot create file '/usr/local/Cellar/r/3.6.1_1/lib/R/doc/html/packages.html', reason 'Permission denied'
Warning in install.packages :
cannot update HTML package index
As stated here by RStudio Support:
Are you able to install packages in R?
If you're having issues, we recommend trying to install packages in R
(outside of RStudio) and see if you're able to do that. If not, please
check the possible solutions below.
Therefore, one needs to:
switch to Terminal.app,
while inside your Terminal, your R console must be started with the sudo privileges. Otherwise, it will yet again fail with a permission denied error. Hence, inside your Terminal, type sudo R,
and then install whatever package is necessary: e.g. install.packages("mlbench").
Related
I'm trying to run this piece of code from a Github read.me file
## Install
```{r,eval=FALSE}
#install.packages('devtools')
devtools::install_github('jeff324/powder',build_vignettes = TRUE)
```
However. I keep getting this error message back in the console:
Downloading GitHub repo jeff324/powder#HEAD
Installing 1 packages: tibble
Installing package into ‘C:/Users/tessc/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/tibble_3.0.6.zip'
Content type 'application/zip' length 836388 bytes (816 KB)
downloaded 816 KB
package ‘tibble’ successfully unpacked and MD5 sums checked
Error: Failed to install 'powder' from GitHub:
(converted from warning) cannot remove prior installation of package ‘tibble’
>
Does anyone know what might be happening?
First thing I do when I get these types of errors is to Restart R. Go to Session -> Restart R. If that doesn't work, try opening a brand new session in R Studio. I was just able to install this package. So fundamentally, it is working.
I'm having trouble installing the vcfR package in R studio.
I'm on Ubuntu 18.04.4 LTS in Rstudio and my R version 3.6.3
When I try to install using:
install.packages('vcfR')
I get a non-zero exit status
Installing package into ‘/home/username/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'http://cran.r-project.org/src/contrib/vcfR_1.11.0.tar.gz'
Content type 'application/x-gzip' length 1453180 bytes (1.4 MB)
==================================================
downloaded 1.4 MB
* installing *source* package ‘vcfR’ ...
** package ‘vcfR’ successfully unpacked and MD5 sums checked
** using staged installation
./configure: 4: ./configure: checkbashisms: not found
Warning in system(cmd) : error in running command
ERROR: configuration failed for package ‘vcfR’
* removing ‘/home/username/x86_64-pc-linux-gnu-library/3.6/vcfR’
Warning in install.packages :
installation of package ‘vcfR’ had non-zero exit status
I'm not really sure where to go from here or what to try to fix it.
This would appear to be due to a simple bug in the package vcfR. In the most recent version its configure script consists of
#!/bin/sh
#
checkbashisms --force
# EOF.
which makes little to no sense. CRAN never noticed because they now have the script checkbashishm (from Debian's devscript package) installed. Someone should tell the maintainer of vcfR to correct this. I'll send him a mail. At a minimum it should change to
if [ -f /usr/bin/checkbashisms ]; then
checkbashisms --force
fi
I found this on github, so apparently it is a general issue:
https://github.com/r-hub/rhub-linux-builders/issues/46
I'm also running Ubuntu 18.04.04, and got the same error message as you. I installed the devscripts package through the terminal using the following code:
sudo apt update
sudo apt install devscripts
I was then able to successfully install vcfR in RStudio.
I just updated R to 3.4.0 and RStudio to 1.0.143, and I reinstalled some packages. Everything was ok except for Rcpp (and packages which require Rccp), I got this :
> install.packages("Rcpp")
Warning in install.packages :
cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES.rds': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.4/PACKAGES.rds': HTTP status was '404 Not Found'
There is a binary version available but the source version is later:
binary source needs_compilation
Rcpp 0.12.10 0.12.11 TRUE
Do you want to install from sources the package which needs compilation?
y/n: y
installing the source package ‘Rcpp’
trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_0.12.11.tar.gz'
Content type 'application/x-gzip' length 2485092 bytes (2.4 MB)
downloaded 2.4 MB
'\\CXXXX0001\Users\RXXXXn'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
'\\CXXXX0001\Users\RXXXXn\R\R-3.4.0' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"//CXXXX0001/Users/RXXXn/R/R-3.4.0/bin/x64/R" CMD INSTALL -l "\\CXXXX0001\Users\RXXXXn\R\R-3.4.0\library" C:\Users\RXXX~1\AppData\Local\Temp\RtmpmOL8r0/downloaded_packages/Rcpp_0.12.11.tar.gz' had status 1
Warning in install.packages :
installation of package ‘Rcpp’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\RXXXXn\AppData\Local\Temp\RtmpmOL8r0\downloaded_packages’
I restarted my R session before doing this, so there should be no conflict of loaded packages.
What can I do ?
EDIT after user3293236 comment
I also have a problem with devtools package...
> install.packages("devtools")
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/devtools_1.13.1.zip'
Content type 'application/zip' length 440923 bytes (430 KB)
downloaded 430 KB
package ‘devtools’ successfully unpacked and MD5 sums checked
Warning in install.packages :
unable to move temporary installation ‘\\CXXXX0001\Users\RXXXXn\R\R-3.4.0\library\file16401ac3a13\devtools’ to ‘\\CXXXX0001\Users\RXXXXn\R\R-3.4.0\library\devtools’
The downloaded binary packages are in
C:\Users\RXXXXn\AppData\Local\Temp\RtmpmOL8r0\downloaded_packages
> library(devtools)
Error in library(devtools) : aucun package nommé ‘devtools’ n'est trouvé
I encountered the same issue while trying to set up someone else's computer. Brand new R installation (R version 3.4.1) but R was installed in a OneDrive folder. I also thought it was a permissions thing (as #nrussell commented) as the error was the same ... unable to move temporary installation ....
I had no issue installing devtools as normal (or any other packages) and even with Rtools installed Rcpp would not install by install.packages("Rcpp")`. Interestingly,
install.packages("Rcpp", type = 'source')
Did work after some compiling. Strange...
I had similar problem so, I installed a previous Rcpp release and worked.
install_version("Rcpp", version = "1.0.3", repos = "http://cran.us.r-project.org")
What can you do? I would start by reading the error messages.
It clearly showed you that you are offered a different source and binary version. For the former you need tools. That is abundantly documented.
And by tomorrow CRAN will also have a new binary version for you. But with a new release made hours ago, you need to wait a moment. Or make your system capable of installing from source.
while installing rpackage Roracle on windows 10 i'm getting stuck at this point
install.packages("ROracle")
Installing package into ‘C:/Users/admin/Documents/R/win-library/3.3’
(as ‘lib’ is unspecified)
Package which is only available in source form, and may need compilation of C/C++/Fortran:
‘ROracle’
Do you want to attempt to install these from sources?
y/n: y
installing the source package ‘ROracle’
trying URL 'https://cran.rstudio.com/src/contrib/ROracle_1.3-1.tar.gz'
Content type 'application/x-gzip' length 308252 bytes (301 KB)
downloaded 301 KB
* installing *source* package 'ROracle' ...
** package 'ROracle' successfully unpacked and MD5 sums checked
ERROR: cannot find Oracle Client.
Please set OCI_LIB64 to specify its location.
Warning: running command 'sh ./configure.win' had status 1
ERROR: configuration failed for package 'ROracle'
* removing 'C:/Users/admin/Documents/R/win-library/3.3/ROracle'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\admin\Documents\R\win-library\3.3" C:\Users\admin\AppData\Local\Temp\RtmpGYlz5L/downloaded_packages/ROracle_1.3-1.tar.gz' had status 1
Warning in install.packages :
installation of package ‘ROracle’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\admin\AppData\Local\Temp\RtmpGYlz5L\downloaded_packages’
I've installed Rtools Rtools33.exe and my R version is version.string R version 3.3.2 (2016-10-31)
please help to connect it with oracle 11g database
Oracle client is intalled in d drive which path is:
D:\app\admin\product\11.2.0\client_1\BIN
As #Nathan Dobie mentionned, instructions on the ROracle installation were helpful for me. I didn't need Rtools.exe but i had to add oracle instant client in the Environment variables.
Configuration in 64bits:
Under System variables, create OCI_LIB64 if it does not already exist.
Set the value of OCI_LIB64 to D:\app\admin\product\11.2.0\client_1\BIN (in your case)
Under System variables, edit PATH to include
D:\app\admin\product\11.2.0\client_1\BIN
And you will also need to create OCI_INC with the following value
D:\app\admin\product\11.2.0\client_1\oci\include
Worked very well for me :-)
I followed the instructions on randyzwitch's blog (http://randyzwitch.com/r-amazon-ec2/) to install r-studio server on ec2 instance running ubuntu 12.04.
When I start r-studio server and try to install packages, this is what was happening:
> install.packages("dplyr")
Warning in install.packages :
package ‘dplyr’ is not available (for R version 2.14.1)
Installing package(s) into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Warning in install.packages :
'lib = "/usr/local/lib/R/site-library"' is not writable
Would you like to create a personal library
~/R/x86_64-pc-linux-gnu-library/2.14
to install packages into? (y/n) y
Warning in install.packages :
package ‘dplyr’ is not available (for R version 2.14.1)
I realized I need to update R so I checked out this post and updated it: https://askubuntu.com/questions/218708/installing-latest-version-of-r-base/436491#436491
I am logged in as sudo user. When I try to install package now, i get this:
> install.packages("plyr")
Installing package into ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
also installing the dependency ‘Rcpp’
trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.11.5.tar.gz'
Content type 'application/x-gzip' length 2353791 bytes (2.2 MB)
==================================================
downloaded 2.2 MB
trying URL 'http://cran.rstudio.com/src/contrib/plyr_1.8.2.tar.gz'
Content type 'application/x-gzip' length 392136 bytes (382 KB)
==================================================
downloaded 382 KB
Warning in install.packages :
system call failed: Cannot allocate memory
Warning in install.packages :
installation of package ‘Rcpp’ had non-zero exit status
Warning in install.packages :
system call failed: Cannot allocate memory
Warning in install.packages :
installation of package ‘plyr’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp6Kgx5d/downloaded_packages’
I saw this post : lme4 package install failing on Ubuntu 12.04 and followed all instructions but it didn't solve the problem. Still same result. Thoroughly frustrated with trying to run rstudio server on aws. Someone please help!
Are you using the instance type t2.micro? Try using a more powerful instance with more RAM, that worked for me.
Please make sure you are root user when installing packages:
sudo su command will take you to root user. Then run your install package code.
or use sudo before run you script: sudo Rscript 1.R