Question: DelayedArray install fails to UNC path
0
gravatar for simon.andrews
16 months ago by
simon.andrews0 wrote:

We have a software package which automates the installation of some R packages and automatically reports failures.  We've recently seen a few related reports which are all in the installation of the DelayedArray package, and are the result of a failure to install one of the documentation files.

The common factor is that in each case R is installed to a windows share accessed via a UNC path.  In the error the path which is constructed appears to be a mix or forward and reverse slashes, and I think this might be what is causing the ultimate failure.

This problem seems to be limited to DelayedArray.  Other packages are installing OK on the same systems.

I don't have full system information for these failures as I'm getting these reports through our automated crash reporters and I've not reproduced this on our own systems, but hopefully there's enough information in the trace below to identify and fix the root cause.

R version 3.5.0 (2018-04-23) -- "Joy in Playing"
trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/DelayedArray_0.6.1.tar.gz'
Content type 'application/x-gzip' length 485768 bytes (474 KB) ==================================================

downloaded 474 KB
* installing *source* package 'DelayedArray' ...
** R
** inst
** byte-compile and prepare package for lazy loading Creating a new generic function for 'aperm' in package 'DelayedArray'
in method for 'coerce' with signature '"DelayedMatrix","dgCMatrix"': no definition for class "dgCMatrix"
in method for 'coerce' with signature '"DelayedMatrix","sparseMatrix"': no definition for class "sparseMatrix"
Creating a generic function for 'sweep' from package 'base' in package 'DelayedArray'
Creating a new generic function for 'apply' in package 'DelayedArray'
Creating a generic function for 'dnorm' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'pnorm' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qnorm' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'dbinom' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'pbinom' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qbinom' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'dpois' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'ppois' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qpois' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'dlogis' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'plogis' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qlogis' from package 'stats' in package 'DelayedArray'
Creating a new generic function for 'rowMaxs' in package 'DelayedArray'
Creating a new generic function for 'colMaxs' in package 'DelayedArray'
Creating a new generic function for 'rowMins' in package 'DelayedArray'
Creating a new generic function for 'colMins' in package 'DelayedArray'
Creating a new generic function for 'rowRanges' in package 'DelayedArray'
Creating a new generic function for 'colRanges' in package 'DelayedArray'
** help
*** installing help indices
  converting help for package 'DelayedArray'
    finding HTML links ... done
    Array-class                             html
    ArrayGrid-class                         html
    DelayedArray-class                      html
Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-class.Rd:205: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
    DelayedArray-stats                      html
Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-stats.Rd:60: file link 'dnorm' in package 'stats' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-stats.Rd:60: file link 'dbinom' in package 'stats' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-stats.Rd:61: file link 'dpois' in package 'stats' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-stats.Rd:61: file link 'dlogis' in package 'stats' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-stats.Rd:68: file link 'dnorm' in package 'stats' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-stats.Rd:68: file link 'dbinom' in package 'stats' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-stats.Rd:69: file link 'dpois' in package 'stats' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-stats.Rd:69: file link 'dlogis' in package 'stats' does not exist and so has been treated as a topic

    DelayedArray-utils                      html

Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-utils.Rd:99: file link 'Ops' in package 'methods' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-utils.Rd:100: file link 'Math' in package 'methods' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-utils.Rd:100: file link 'Math2' in package 'methods' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-utils.Rd:119: file link 'Summary' in package 'methods' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-utils.Rd:133: file link 'is.na' in package 'base' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-utils.Rd:133: file link '!' in package 'base' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-utils.Rd:135: file link '%*%' in package 'base' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-utils.Rd:138: file link 'rowSums' in package 'base' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-utils.Rd:139: file link 'rowMaxs' in package 'matrixStats' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-utils.Rd:158: file link 'Ops' in package 'methods' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-utils.Rd:159: file link 'Math' in package 'methods' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/DelayedArray-utils.Rd:159: file link 'Math2' in package 'methods' does not exist and so has been treated as a topic

    DelayedOp-class                         html
    RleArray-class                          html

Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/RleArray-class.Rd:68: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/RleArray-class.Rd:91: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/RleArray-class.Rd:103: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic

    bind-arrays                             html

Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/bind-arrays.Rd:40: file link 'rbind' in package 'base' does not exist and so has been treated as a topic

    block_processing                        html
    extract_array                           html

Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/extract_array.Rd:46: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/someuser/AppData/Local/Temp/Rtmp6ZPoih/R.INSTALL26286ec75aa9/DelayedArray/man/extract_array.Rd:103: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic

    realize                                 html
    showtree                                html

** building package indices
** installing vignettes
Warning in file(con, "w") :

  cannot open file '\\WIN-SERVER/Users$/someuser/My Documents/R/win-library/3.5/DelayedArray/doc/index.html': No such file or directory Error in file(con, "w") : cannot open the connection

ERROR: installing vignettes failed

* removing '\\WIN-SERVER/Users$/someuser/My Documents/R/win-library/3.5/DelayedArray'

In R CMD INSTALL

 

 

installation bug delayedarray • 352 views
ADD COMMENTlink modified 15 months ago by Martin Morgan ♦♦ 24k • written 16 months ago by simon.andrews0
Answer: DelayedArray install fails to UNC path
0
gravatar for Martin Morgan
15 months ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

This \\WIN-SERVER/Users$/someuser/My Documents/R/win-library looks like your R is trying to use a 'UNC' path. The solution / workaround is to map your network drive to a letter (google for that), e.g., X:\\ then update the way you launch R so that it uses this path, perhaps updating the shortcut you click on to use the mapped drive.

ADD COMMENTlink written 15 months ago by Martin Morgan ♦♦ 24k
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