DelayedArray install fails to UNC path
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@simonandrews-16386
Last seen 3.3 years ago

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) ==================================================

* 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'
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

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

delayedarray bug installation • 506 views
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Entering edit mode
@martin-morgan-1513
Last seen 3 months ago
United States

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.