Failure to install on Windows R3.6.1

[Tongtong-Wang]

Hi, Farrellja

Thanks for such a wonderful package, I'm having problems with installing it on my windows x64 platform with R version of 3.6.1

The following is what I have as error messages, please help

devtools::install_github(repo="farrellja/URD") Downloading GitHub repo farrellja/URD@master Skipping 1 packages not available: destiny √ checking for file 'C:\Users\a1189099\AppData\Local\Temp\Rtmp2Jj8SP\remotes1054cc563d6\farrellja-URD-cb6d83f/DESCRIPTION' ...

• preparing 'URD': (1.5s) √ checking DESCRIPTION meta-information ...
• checking for LF line-endings in source and make files and shell scripts (1.2s)
• checking for empty or unneeded directories
• building 'URD_1.1.0.tar.gz' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-10-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-11-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-12-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-13-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-13-2.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-13-3.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-14-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-15-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-15-2.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-15-3.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-17-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-17-2.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-17-3.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-17-4.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-17-5.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-18-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-18-2.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-2-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-2-2.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-2-3.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-2-4.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-20-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-21-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-22-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-3-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-4-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-4-2.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-4-3.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-6-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-7-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/QuickStart/URD-QuickStart-AxialMesoderm_files/figure-markdown_github/unnamed-chunk-9-1.png' Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: 'URD/Analyses/SupplementaryAnalysis/URD-11-BatchModuleRemovalAndClusteringAnalysisOfSmartseqDataset.Rmd'

Installing package into ‘C:/R_lib’ (as ‘lib’ is unspecified) '\UOFA\USERS$\users9\a1189099' CMD.EXE was started with the above path as the current directory. UNC paths are not supported. Defaulting to Windows directory.

• installing source package 'URD' ... using staged installation R Error : (converted from warning) unable to re-encode 'NMFDoublets.R' line 297 ERROR: unable to collate and parse R files for package 'URD'
• removing 'C:/R_lib/URD' Error: Failed to install 'URD' from GitHub: (converted from warning) installation of package ‘C:/Users/a1189099/AppData/Local/Temp/Rtmp2Jj8SP/file10546d122651/URD_1.1.0.tar.gz’ had non-zero exit status In addition: Warning messages: 1: In untar2(tarfile, files, list, exdir) : skipping pax global extended headers 2: In untar2(tarfile, files, list, exdir) : skipping pax global extended headers

I actually have all dependent packages, which I don't really know what to do at this point. I've updated my R, and still the same message popped up. Thanks in advance!

[farrellja]

@Tongtong-Wang Hey -- I've never seen this issue before. I have not tried to install URD on R 3.6.x yet. Two things stand out to me:

1. Skipping 1 packages not available: destiny -- URD cannot/will not install if a functional installation of destiny is not present. Double check that it is properly installed; if not, that's the first thing to try to take care of.
2. Error : (converted from warning) unable to re-encode 'NMFDoublets.R' line 297 -- I wonder if there is a corrupt download of the files? Try deleting the temp files (they seem to be located here: C:\Users\a1189099\AppData\Local\Temp\Rtmp2Jj8SP\remotes1054cc563d6\farrellja-URD-cb6d83f) and try re-installing.
3. If that continues to be a problem, let me know -- there is a non-ASCII character in that line of code (a plot is labeled with "Δ Overlap:") and maybe depending on the configuration of your operating system this can pose a problem? If 1 & 2 don't fix it, let me know, and I'll try changing this line of code.

[Tongtong-Wang]

Hi, Farrellja

I’ve figured out eventually, it turns out my Rcpp package was corrupted during my last attempt to updating R from 3.5.x to 3.6.x after reinstalling Rcpp by loading the tarball in, URD is then also installable. Although I have to use the tarball to do that. For some reasons, those few packages do not install from either bioconductor nor GitHub. Thanks for your speedy reply!