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I am trying to install several packages that go with Rcistarget.

BiocManager::install(c("doMC", "doRNG"), force=TRUE) BiocManager::install(c("DT", "visNetwork"), force=TRUE)

Only "doRNG" works, the other three fail and continue to give me an error saying it is not available for my version of Bioconductor (version 3.15) and that some other packages cannot be updated.

I have two questions with this:

  1. How do I find out the version of Bioconductor needed for a package to be installed?
  2. When I manually installed the dependencies, there were no issues but trying to install those three packages, again continued to say there were issues.

This is what I did:

> BiocManager::install(c("DT", "visNetwork"), force=TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.19), R 4.2.0 (2022-04-22 ucrt)
Installing package(s) 'DT', 'visNetwork'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/DT_0.26.zip'
Content type 'application/zip' length 1839666 bytes (1.8 MB)
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/visNetwork_2.1.2.zip'
Content type 'application/zip' length 4700067 bytes (4.5 MB)
downloaded 4.5 MB

package ‘DT’ successfully unpacked and MD5 sums checked
package ‘visNetwork’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\kathe\AppData\Local\Temp\Rtmpcdo34f\downloaded_packages
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.2.0/library
  packages:
    boot, cluster, foreign, MASS, Matrix, mgcv, nlme, nnet, rpart, survival

But, when I manually installed packages boot, cluster, foreign, etc....they were all fine.

> install.packages(c("boot","cluster","foreign","MASS","Matrix","mgcv","nlme","nnet","rpart","survival"))
package ‘boot’ successfully unpacked and MD5 sums checked
package ‘cluster’ successfully unpacked and MD5 sums checked
package ‘foreign’ successfully unpacked and MD5 sums checked
package ‘MASS’ successfully unpacked and MD5 sums checked
package ‘Matrix’ successfully unpacked and MD5 sums checked
package ‘mgcv’ successfully unpacked and MD5 sums checked
package ‘nlme’ successfully unpacked and MD5 sums checked
package ‘nnet’ successfully unpacked and MD5 sums checked
package ‘rpart’ successfully unpacked and MD5 sums checked
package ‘survival’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\kathe\AppData\Local\Temp\Rtmpcdo34f\downloaded_packages

However, if I run BioManager::install("DT","VisNetwork"), force=TRUE) as an example, it continues to produce the same error.

What can I do to fix this? The R version I have is 4.2.0 in RStudio.

Katherine Chau
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  • Maybe try contacting the package's author on `GitHub`. – Ed_Gravy Nov 30 '22 at 16:06
  • It seems odd that it's trying to write to `C:/Program Files/R/R-4.2.0/library`. Normally R uses user specific library folders. Have you customized your `.libPaths()`? Are you running as administrator or something? – MrFlick Nov 30 '22 at 16:30
  • Nope I haven't done anything to change my libPaths or messed around with anything. Recently I managed to install other packages without issue for another program. Only this one is suddenly giving me issues. – Katherine Chau Nov 30 '22 at 16:34
  • this basically seems like a dup of https://stackoverflow.com/questions/41839214/installation-path-not-writable-r-unable-to-update-packages. What you tried any of those suggestions? What does `.libPaths()` return? What about `table(installed.packages()[, "LibPath"])` – MrFlick Nov 30 '22 at 17:54
  • The error message is "Installation paths not writeable, unable to update packages", I don't see the message you described in your text. – user2554330 Nov 30 '22 at 18:20

0 Answers0