Question: 'Codetools' and 'mgcv' packages fail to update
0
gravatar for pbhamidipati
4.2 years ago by
United States
pbhamidipati0 wrote:

(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
ADD COMMENTlink modified 4.1 years ago by rodrigo_sengo0 • written 4.2 years ago by pbhamidipati0
Answer: 'Codetools' and 'mgcv' packages fail to update
1
gravatar for Dan Tenenbaum
4.2 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:

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.

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Dan Tenenbaum8.2k

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

- Pranav

ADD REPLYlink written 4.2 years ago by pbhamidipati0

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

ADD REPLYlink written 4.2 years ago by Dan Tenenbaum8.2k

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 

ADD REPLYlink written 4.1 years ago by rodrigo_sengo0

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

ADD REPLYlink written 4.1 years ago by Dan Tenenbaum8.2k

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

ADD REPLYlink written 3.9 years ago by mk.applebee0
Answer: 'Codetools' and 'mgcv' packages fail to update
0
gravatar for rodrigo_sengo
4.1 years ago by
Portugal
rodrigo_sengo0 wrote:

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

ADD COMMENTlink written 4.1 years ago by rodrigo_sengo0

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

 

ADD REPLYlink written 4.1 years ago by Dan Tenenbaum8.2k
Answer: 'Codetools' and 'mgcv' packages fail to update
0
gravatar for rodrigo_sengo
4.1 years ago by
Portugal
rodrigo_sengo0 wrote:

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] 

ADD COMMENTlink written 4.1 years ago by rodrigo_sengo0

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.

ADD REPLYlink written 4.1 years ago by Dan Tenenbaum8.2k
Answer: 'Codetools' and 'mgcv' packages fail to update
0
gravatar for rodrigo_sengo
4.1 years ago by
Portugal
rodrigo_sengo0 wrote:

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

 

ADD COMMENTlink written 4.1 years ago by rodrigo_sengo0
Answer: 'Codetools' and 'mgcv' packages fail to update
0
gravatar for Dan Tenenbaum
4.1 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:

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.

 

ADD COMMENTlink written 4.1 years ago by Dan Tenenbaum8.2k
Answer: 'Codetools' and 'mgcv' packages fail to update
0
gravatar for rodrigo_sengo
4.1 years ago by
Portugal
rodrigo_sengo0 wrote:

Finaly I have it! Thank you so much! 

ADD COMMENTlink written 4.1 years ago by rodrigo_sengo0
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