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About r : installation-path-not-writable-R-unable-to-update-packages

Question Detail

I am trying to install Bioconductor into R, using the code on their website. When I type in the code (see bellow) I get an error message saying that some packages can’t be updated, the installation path is unwriteable.

> ## try http:// if https:// URLs are not supported
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
installation path not writeable, unable to update packages: Matrix, mgcv,

survival

I can install these package by going to packages/install packages.

> utils:::menuInstallPkgs()
trying URL    'https://www.stats.bris.ac.uk/R/bin/windows/contrib/3.3/Matrix_1.2-8.zip'
Content type 'application/zip' length 2775038 bytes (2.6 MB)
downloaded 2.6 MB

trying URL 'https://www.stats.bris.ac.uk/R/bin/windows/contrib/3.3/mgcv_1.8-  16.zip'
Content type 'application/zip' length 2346257 bytes (2.2 MB)
downloaded 2.2 MB

trying URL     'https://www.stats.bris.ac.uk/R/bin/windows/contrib/3.3/survival_2.40-1.zip'
Content type 'application/zip' length 5109948 bytes (4.9 MB)
downloaded 4.9 MB

package ‘Matrix’ successfully unpacked and MD5 sums checked
package ‘mgcv’ successfully unpacked and MD5 sums checked
package ‘survival’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\stxeb8\AppData\Local\Temp\Rtmp2tQZ4v\downloaded_packages

I can then go to packages/ load packages and load them succesfully and search and see that the packages are there.

> local({pkg <- select.list(sort(.packages(all.available =   TRUE)),graphics=TRUE)
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
Loading required package: nlme
This is mgcv 1.8-16. For overview type 'help("mgcv-package")'.
> local({pkg <- select.list(sort(.packages(all.available = TRUE)),graphics=TRUE)
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
> local({pkg <- select.list(sort(.packages(all.available = TRUE)),graphics=TRUE)
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
> local({pkg <- select.list(sort(.packages(all.available =     TRUE)),graphics=TRUE)
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
> search()
[1] ".GlobalEnv"            "package:survival"      "package:mgcv"         
[4] "package:nlme"          "package:Matrix"        "package:BiocInstaller"
[7] "package:stats"         "package:graphics"      "package:grDevices"    
[10] "package:utils"         "package:datasets"      "package:methods"      
[13] "Autoloads"             "package:base"         

But then when I go to install bioconductor it gives me the same error message that Matrix, mgcv and survival aren’t able to be updated.

> ## try http:// if https:// URLs are not supported
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
installation path not writeable, unable to update packages: Matrix, mgcv,
  survival

What can I do to be able to update these packages so I can install bioconductor?

Question Answer

In general, I would advise against changing the permission in system folders, because R should work without additional administrative rights.

Thus I would likewise advise against installing packages using administrative rights, as you would be required to do so in the future every time you have to update these packages!

To backtrace this issue and prevent to minimize it in future updates, you should perform the following steps:

  1. Note which packages that fail to update (already shown in the error message).
  2. Locate the folders where all R packages are installed using .libPaths(). This should provide two results, a destination in your home folder and a system folder.

“/home/USER/R/x86_64-pc-linux-gnu-library/X.X” “/usr/lib/R/library”

  1. Install the packages with install.packages(c("PKG1", "PKG2", "PKG3")) or BiocManager::install(c("PKG1", "PKG2", "PKG3"))*
  2. Only If you have administrator rights: Manually remove the older package folders from the system folder (“/usr/lib/R/library”), using administrator rights (sudo) OR enter R with administrator rights One last time and run remove.packages(c("PKG1", "PKG2", "PKG3"), lib = "/usr/lib/R/library").

*If there are issues with the installation path, add the argument , lib = "/home/USER/R/x86_64-pc-linux-gnu-library/X.X" to either of the install functions in step 3. This argument explicitly states to install in your home folder.

There is a single issue with this approach, at least with the official R repository on Arch Linux: Whenever R is updated, the updated version still includes packages in the system folder, that can’t be updated without administrative rights. Therefore for each R update, this procedure must be repeated. I’m especially looking at you survival!!!

*Edit: It is important to note that biocLite is no longer the recommended tool for installing BioConductor packages. You should instead use BiocManager, which is in the official CRAN repository (install.packages("BiocManager")).

**Second edit: As this answer still receives votes, I have updated and cleaned up the answer.

It was a permission issue for me. First, I identified where the packages were installed using installed.packages()[, c("Package", "LibPath")]. This outputs a long 2 column matrix with the names and locations of the packages. Then you will see where the offending packages are. In my case, they were at /usr/lib/R/site-library and /usr/lib/R/library. Then I changed the permission of these folders by chmod (I used chmod -R 777 on the main R folder, this is my personal computer, so security is not a big concern here I think).

If you are running R/Rstudio on Windows, then just open R/Rstudio as administrator. Right click on the icon then run as administrator

It looks like several ‘recommended’ packages are installed in two places — maybe by an administrator account in a directory you don’t have write access to, and then by RStudio in a directory where you do have write access. biocLite() is complaining about the former.

Unless biocLite() complains about a Bioconductor package that cannot be installed (different from cannot be updated), there is no problem and basic Bioconductor packages have been successfully installed. Check out https://support.bioconductor.org for future Bioconductor-related support.

One solution is to open a terminal and load R using admin rights

sudo R
update.packages()
source("https://bioconductor.org/biocLite.R")
biocLite()

Then you can update. But careful. This can create packages by the admin in a directory supposed to be owned by a user.

In this case, instead of loading R as root (which is solving the problem until the next update), check the .libPaths(). You will have a list of directories.

.libPaths()
"/home/it_s_me/R/x86_64-pc-linux-gnu-library/3.4" "/usr/lib/R/library"

In my case, all packages in “/usr/lib/R/library” are owned by root, and all except one are owned by a normal user (not root) at “/home/itsame/R/x86_64-pc-linux-gnu-library/3.4”.

If you have admin rights, an easy solution may be to run chown in all the places: For example, I had trouble updating the curl package. I used:

sudo chown -R it_s_me /home/it_s_me/R/x86_64-pc-linux-gnu-library/3.4/curl/

I had a similar problem with other Bioconductor packages and the solution was simpler than I thought. I had to install some OS packages pointed out on my log: libcurl-dev, libcurl4-openssl-dev, libssl-dev.

My advice is to check your R log and look for “Configuration failed because [PACKAGE] was not found. Try installing”.

Since with the version of R 3.6.1 the script http://bioconductor.org/biocLite.R returns this message ” Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install ” I solved the problem with the following steps:

  1. Get the list of directories used by R to install libraries and
    choose the one with write permissions using: .libPaths()
  2. Installing the “BiocManager” library using: install.packages("BiocManager")
  3. Installation of the library “bioconductor” by forcing the directory
    with write permissions using: BiocManager::install("Rgraphviz", lib = "C:/Users/tizbet/Documents/R/win-library/3.6")

I worked on the following R installation:

platform x86_64-w64-mingw32, arch x86_64, os mingw32, system x86_64, mingw32, version.string R version 3.6.1 (2019-07-05)

I was inspired by the Kasper Thystrup Karstensen answer

Try to add the argument force = TRUE :

BiocManager::install("XX", force = TRUE )

Whenever you want to work on an R-code where packages need to be installed: –

  • Windows: Open R-studio as ‘Run as administrator’ [Right click on the icon]
  • Linux: Run as sudo user; else get writing rights from the administrator

Ubuntu:

sudo apt install libcurl-dev

Fedora:

sudo dnf install libcurl-devel

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