'Codetools' and 'mgcv' packages fail to update
6
0
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@pbhamidipati-7481
Last seen 6.5 years ago
United States

(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
package updates codetools deseq mgcv • 3.9k views
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1
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 7 months ago
United States

After you answer 'y' to the questions about codetools and mgcv, a dialog should pop up saying "Would you like to use a personal library instead?" Be sure and answer Yes to this and it should update codetools and mgcv.

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0
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Thanks! I wasn't able to use the command line after the warning printed, but now it works.

- Pranav

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Note that I modified my original answer to be more accurate, but I'm glad you got it working.

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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 

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0
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What operating system are you on? Can you post your sessionInfo()?

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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

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@rodrigo_sengo-7575
Last seen 6.4 years ago
Portugal

I am using Vista 64 bits. 

My session info: 

sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Portuguese_Portugal.1252  LC_CTYPE=Portuguese_Portugal.1252   
[3] LC_MONETARY=Portuguese_Portugal.1252 LC_NUMERIC=C                        
[5] LC_TIME=Portuguese_Portugal.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_2.14.2

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0
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Can you post the full output of biocLite('mgcv')?

 

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@rodrigo_sengo-7575
Last seen 6.4 years ago
Portugal

biocLite('mgcv')
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Installing package(s) 'mgcv'
Installing package(s) into ‘C:/Users/Oem/Documents/R/win-library/2.14’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/bin/windows/contrib/2.14/mgcv_1.7-22.zip'
Content type 'application/zip' length 1482275 bytes (1.4 Mb)
opened URL
downloaded 1.4 Mb

package ‘mgcv’ successfully unpacked and MD5 sums checked

The downloaded packages are in
    C:\Users\Oem\AppData\Local\Temp\RtmpaAVJOz\downloaded_packages
Warning message:
'boot' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.2/library' not writeable
'class' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.2/library' not writeable
'cluster' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.2/library' not writeable
'foreign' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.2/library' not writeable
'KernSmooth' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.2/library' not writeable
'lattice' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.2/library' not writeable
'MASS' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.2/library' not writeable
'Matrix' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.2/library' not writeable
'nlme' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.2/library' not writeable
'nnet' cannot be updated, installed directory 'C:/Program Files/R/R-2.14.2/library' not writeable
'r [... truncated] 

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0
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That's not the complete output. It looks from the partial output that mgcv was installed, but I could be wrong. What does

packageVersion('mgcv')

say? If it says 1.7.22, then you have the most recent version of mgcv.

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@rodrigo_sengo-7575
Last seen 6.4 years ago
Portugal

Yes I have the ,mgcv package installed and the version is 1.7.22, but recently the autor of this package created a new version (version 1.8-5). please see: https://stat.ethz.ch/R-manual/R-devel/library/mgcv/html/00Index.html

 

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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 7 months ago
United States

Actually there is a version 1.8.6 (see http://cran.rstudio.com/web/packages/mgcv/index.html). To get it you should update to R-3.1.3.

 

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@rodrigo_sengo-7575
Last seen 6.4 years ago
Portugal

Finaly I have it! Thank you so much! 

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