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Question: [Windows 10] 64. Problem installing biocLite due Warning on non writable directory
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gravatar for juancaf
24 months ago by
juancaf0
juancaf0 wrote:

I got a Warning message when installing on Windows 10, 64b. After the warning message the installation stopped. The warning message said that the lib directory is not writable. I triend on the fly to change permisions on the directory but the problem is that I don´t know which user is actually installing the packages.

The installation log is the following

> source("https://www.bioconductor.org/biocLite.R")
Installing package into ‘C:/Users/ElverGonsanama/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/BiocInstaller_1.20.1.zip'
Content type 'application/zip' length 116689 bytes (113 KB)
downloaded 113 KB

package ‘BiocInstaller’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\ElverGonsanama\AppData\Local\Temp\RtmpqaDlwk\downloaded_packages
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for
  help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.2
  (2015-08-14).
Installing package(s) ‘Biobase’, ‘IRanges’, ‘AnnotationDbi’
also installing the dependencies ‘BiocGenerics’, ‘S4Vectors’, ‘DBI’, ‘RSQLite’

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/BiocGenerics_0.16.1.zip'
Content type 'application/zip' length 962958 bytes (940 KB)
downloaded 940 KB

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/S4Vectors_0.8.3.zip'
Content type 'application/zip' length 1748182 bytes (1.7 MB)
downloaded 1.7 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/DBI_0.3.1.zip'
Content type 'application/zip' length 162585 bytes (158 KB)
downloaded 158 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/RSQLite_1.0.0.zip'
Content type 'application/zip' length 1217716 bytes (1.2 MB)
downloaded 1.2 MB

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/Biobase_2.30.0.zip'
Content type 'application/zip' length 4227858 bytes (4.0 MB)
downloaded 4.0 MB

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/IRanges_2.4.2.zip'
Content type 'application/zip' length 3099053 bytes (3.0 MB)
downloaded 3.0 MB

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/AnnotationDbi_1.32.0.zip'
Content type 'application/zip' length 9471800 bytes (9.0 MB)
downloaded 9.0 MB

package ‘BiocGenerics’ successfully unpacked and MD5 sums checked
package ‘S4Vectors’ successfully unpacked and MD5 sums checked
package ‘DBI’ successfully unpacked and MD5 sums checked
package ‘RSQLite’ successfully unpacked and MD5 sums checked
package ‘Biobase’ successfully unpacked and MD5 sums checked
package ‘IRanges’ successfully unpacked and MD5 sums checked
package ‘AnnotationDbi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\ElverGonsanama\AppData\Local\Temp\RtmpqaDlwk\downloaded_packages
Old packages: 'stringi', 'testthat', 'class', 'foreign',
  'MASS', 'mgcv', 'nlme', 'nnet', 'spatial'
Update all/some/none? [a/s/n]:
a
also installing the dependency ‘praise’

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/praise_1.0.0.zip'
Content type 'application/zip' length 17669 bytes (17 KB)
downloaded 17 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/stringi_1.0-1.zip'
Content type 'application/zip' length 14265659 bytes (13.6 MB)
downloaded 13.6 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/testthat_0.11.0.zip'
Content type 'application/zip' length 263584 bytes (257 KB)
downloaded 257 KB

package ‘praise’ successfully unpacked and MD5 sums checked
package ‘stringi’ successfully unpacked and MD5 sums checked
package ‘testthat’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\ElverGonsanama\AppData\Local\Temp\RtmpqaDlwk\downloaded_packages
Warning in install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  'lib = "C:/Program Files/R/R-3.2.2/library"' is not writable

1

This looks like normal behavior. R is installed with a set of core packages in a non-user library (e.g. C:/Program Files/R/R-3.2.2/library):

ip <- installed.packages() 
ip[ip[ ,"Priority"] %in% c("base", "recommended"), c("Package", "Priority")] 

When biocLite() tries to update outdated packages it includes the core packages, whose library can only be written to with administrator privileges; if R isn't launched with those privileges, it will instead try to update to a writable library in the library search path; in your case, that's:

C:/Users/ElverGonsanama/Documents/R/win-library/3.2

Since this user library should precede C:/Program Files/R/R-3.2.2/library in the library search path, it's okay to let R install core-package updates to the user library, because it will thereafter find the most recent versions there first.

If you want updates of the core packages to be written directly to the "core" library, then run R from an elevated command prompt or launch the R GUI with administrator privileges before running biocLite().

ADD REPLYlink written 24 months ago by Jim Java30
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