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Question: biocLite() upgrade issue when same package in 2 libraries
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gravatar for Jenny Drnevich
2.3 years ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k wrote:

Hello,

I've switched to using a personal library in addition to the main library and noticed an issue using biocLite() to update my packages. When I'm not running as administrator, R can't write to the main library but many of the base R packages get upgraded often. Both upgrade.packages() and biocLite() will ask if I want to install the upgrade in my personal library instead, which is nice, neat and efficient. However, biocLite() when run again will still pick up on the old packages in the main library and think they need to be upgraded, whereas upgrade.packges() is slightly better at apparently noticing the newest packages in my personal library, although it just gives an cryptic warning about "package XXX will not be updated". Is there a way to improve biocLite() so that it compares the package versions in the different library trees and only asks about updating if the one in the library called first is outdated? It's not much of a problem the way it is because it does work, it just does a lot of unnecessary downloading and installing or I have to go through and manually figure out which packages to install.

Thanks, Jenny

> .libPaths()
[1] "C:/Users/drnevich/Documents/R/win-library/3.2" "C:/Program Files/R/R-3.2.1/library"           
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.1.
Old packages: 'base64enc', 'BSgenome', 'checkmate', 'nor1mix', 'Rcpp',
  'boot', 'class', 'cluster', 'codetools', 'foreign', 'KernSmooth',
  'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart',
  'spatial', 'survival'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions
  are later:
          binary source needs_compilation
base64enc  0.1-2  0.1-3              TRUE
nor1mix    1.2-0  1.2-1             FALSE

Do you want to install from sources the package which needs compilation?
y/n: y
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/BSgenome_1.36.3.zip'
Content type 'application/zip' length 13100630 bytes (12.5 MB)
downloaded 12.5 MB

# removed a bunch of similar output; at some point a pop-up box appeared about 
# using a personal library instead

package ‘boot’ successfully unpacked and MD5 sums checked
package ‘class’ successfully unpacked and MD5 sums checked
package ‘cluster’ successfully unpacked and MD5 sums checked
package ‘codetools’ successfully unpacked and MD5 sums checked
package ‘foreign’ successfully unpacked and MD5 sums checked
package ‘KernSmooth’ successfully unpacked and MD5 sums checked
package ‘lattice’ 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 ‘spatial’ successfully unpacked and MD5 sums checked
package ‘survival’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\drnevich\AppData\Local\Temp\RtmpAxd1Ae\downloaded_packages

# Now run biocLite() again:

> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.1.
Old packages: 'boot', 'class', 'cluster', 'codetools', 'foreign',
  'KernSmooth', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet',
  'rpart', 'spatial', 'survival'
Update all/some/none? [a/s/n]: 
n

> update.packages()
Warning: package 'boot' in library 'C:/Program Files/R/R-3.2.1/library' will not be updated
Warning: package 'class' in library 'C:/Program Files/R/R-3.2.1/library' will not be updated
Warning: package 'cluster' in library 'C:/Program Files/R/R-3.2.1/library' will not be updated
Warning: package 'codetools' in library 'C:/Program Files/R/R-3.2.1/library' will not be updated
Warning: package 'foreign' in library 'C:/Program Files/R/R-3.2.1/library' will not be updated
Warning: package 'KernSmooth' in library 'C:/Program Files/R/R-3.2.1/library' will not be updated
Warning: package 'lattice' in library 'C:/Program Files/R/R-3.2.1/library' will not be updated
Warning: package 'MASS' in library 'C:/Program Files/R/R-3.2.1/library' will not be updated
Warning: package 'Matrix' in library 'C:/Program Files/R/R-3.2.1/library' will not be updated
Warning: package 'mgcv' in library 'C:/Program Files/R/R-3.2.1/library' will not be updated
Warning: package 'nlme' in library 'C:/Program Files/R/R-3.2.1/library' will not be updated
Warning: package 'nnet' in library 'C:/Program Files/R/R-3.2.1/library' will not be updated
Warning: package 'rpart' in library 'C:/Program Files/R/R-3.2.1/library' will not be updated
Warning: package 'spatial' in library 'C:/Program Files/R/R-3.2.1/library' will not be updated
Warning: package 'survival' in library 'C:/Program Files/R/R-3.2.1/library' will not be updated

> old.packages()
           Package      LibPath                              Installed
boot       "boot"       "C:/Program Files/R/R-3.2.1/library" "1.3-16" 
class      "class"      "C:/Program Files/R/R-3.2.1/library" "7.3-12" 
cluster    "cluster"    "C:/Program Files/R/R-3.2.1/library" "2.0.1"  
codetools  "codetools"  "C:/Program Files/R/R-3.2.1/library" "0.2-11" 
foreign    "foreign"    "C:/Program Files/R/R-3.2.1/library" "0.8-63" 
KernSmooth "KernSmooth" "C:/Program Files/R/R-3.2.1/library" "2.23-14"
lattice    "lattice"    "C:/Program Files/R/R-3.2.1/library" "0.20-31"
MASS       "MASS"       "C:/Program Files/R/R-3.2.1/library" "7.3-40" 
Matrix     "Matrix"     "C:/Program Files/R/R-3.2.1/library" "1.2-1"  
mgcv       "mgcv"       "C:/Program Files/R/R-3.2.1/library" "1.8-6"  
nlme       "nlme"       "C:/Program Files/R/R-3.2.1/library" "3.1-120"
nnet       "nnet"       "C:/Program Files/R/R-3.2.1/library" "7.3-9"  
rpart      "rpart"      "C:/Program Files/R/R-3.2.1/library" "4.1-9"  
spatial    "spatial"    "C:/Program Files/R/R-3.2.1/library" "7.3-9"  
survival   "survival"   "C:/Program Files/R/R-3.2.1/library" "2.38-1" 
           Built   ReposVer  Repository                            
boot       "3.2.1" "1.3-17"  "https://cran.rstudio.com/src/contrib"
class      "3.2.1" "7.3-13"  "https://cran.rstudio.com/src/contrib"
cluster    "3.2.1" "2.0.3"   "https://cran.rstudio.com/src/contrib"
codetools  "3.2.1" "0.2-14"  "https://cran.rstudio.com/src/contrib"
foreign    "3.2.1" "0.8-65"  "https://cran.rstudio.com/src/contrib"
KernSmooth "3.2.1" "2.23-15" "https://cran.rstudio.com/src/contrib"
lattice    "3.2.1" "0.20-33" "https://cran.rstudio.com/src/contrib"
MASS       "3.2.1" "7.3-43"  "https://cran.rstudio.com/src/contrib"
Matrix     "3.2.1" "1.2-2"   "https://cran.rstudio.com/src/contrib"
mgcv       "3.2.1" "1.8-7"   "https://cran.rstudio.com/src/contrib"
nlme       "3.2.1" "3.1-121" "https://cran.rstudio.com/src/contrib"
nnet       "3.2.1" "7.3-10"  "https://cran.rstudio.com/src/contrib"
rpart      "3.2.1" "4.1-10"  "https://cran.rstudio.com/src/contrib"
spatial    "3.2.1" "7.3-10"  "https://cran.rstudio.com/src/contrib"
survival   "3.2.1" "2.38-3"  "https://cran.rstudio.com/src/contrib"

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
[1] BiocInstaller_1.18.4

loaded via a namespace (and not attached):
[1] tools_3.2.1
 

 

ADD COMMENTlink written 2.3 years ago by Jenny Drnevich1.9k

This same question came up yesterday (bioclite lib.loc and R_LIBS_USER. We will discuss improving this.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Dan Tenenbaum ♦♦ 8.2k

I really need to improve my searching abilities - this is twice now in 2 days that I've missed a post on the same question I've had!

Thanks, Jenny

ADD REPLYlink written 2.3 years ago by Jenny Drnevich1.9k
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