Entering edit mode
(Brand new user, please be gentle.)
Just installed R for the first time. I started off by installing the DESeq package, but when it asks to update packages, it gets stalled at the codetools and mgcv packages, spits out the following error and doesn't progress any further:
Warning in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
'lib = "C:/Program Files/R/R-3.1.3/library"' is not writable
Is there a way to bypass this bug or must it be patched?
I tried different combinations of updates and found that 'mgcv' and 'codetools' specifically were causing the issue. Here is one such session illustrating the bug:
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.2), ?biocLite for help
> biocLite("DESeq")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.2), R version 3.1.3.
Installing package(s) 'DESeq'
trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/DESeq_1.18.0.zip'
Content type 'application/zip' length 3020537 bytes (2.9 MB)
opened URL
downloaded 2.9 MB
package ‘DESeq’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Pranav\AppData\Local\Temp\Rtmp2rpBDr\downloaded_packages
Old packages: 'manipulate', 'codetools', 'mgcv'
Update all/some/none? [a/s/n]:
s
manipulate :
Version 0.98.1103 installed in C:/Users/Pranav/Documents/R/win-library/3.1
Version 1.0.1 available at http://cran.rstudio.com
Update (y/N/c)? y
codetools :
Version 0.2-10 installed in C:/Program Files/R/R-3.1.3/library
Version 0.2-11 available at http://cran.rstudio.com
Update (y/N/c)? y
mgcv :
Version 1.8-4 installed in C:/Program Files/R/R-3.1.3/library
Version 1.8-5 available at http://cran.rstudio.com
Update (y/N/c)? y
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.1/manipulate_1.0.1.zip'
Content type 'application/zip' length 35784 bytes (34 KB)
opened URL
downloaded 34 KB
package ‘manipulate’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Pranav\AppData\Local\Temp\Rtmp2rpBDr\downloaded_packages
Warning in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
'lib = "C:/Program Files/R/R-3.1.3/library"' is not writable
Thanks! I wasn't able to use the command line after the warning printed, but now it works.
- Pranav
Note that I modified my original answer to be more accurate, but I'm glad you got it working.
Hi!
I also have the same problem, but in my case no dialog pops up. Could you helpe me? I am interested in the new version of "mgcv", so I can try some gams with zero inflation.
Thank you so much,
Rodrigo Sengo
What operating system are you on? Can you post your
sessionInfo()?Also, the "y" question pops up in a separate windows screen that sometimes appears behind the Rstudio window. I almost gave up thinking that my computer was frozen, and was googling for more solutons when I finally found it and was able to click "Yes" and move on with my life