Back to Books build report for BioC 3.13

BUILD report for OSCA on riesling1

This page was generated on 2021-01-15 16:45:06 -0500 (Fri, 15 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE OSCA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 2/3HostnameOS / ArchINSTALLBUILD
OSCA 1.1.13
Aaron Lun
Snapshot Date: 2021-01-15 09:00:02 -0500 (Fri, 15 Jan 2021)
URL: https://git.bioconductor.org/packages/OSCA
Branch: master
Last Commit: a99ce06
Last Changed Date: 2021-01-04 03:38:38 -0500 (Mon, 04 Jan 2021)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  ERROR 
riesling1 Windows Server 2019 Standard / x64  OK [ ERROR ]

Summary

Package: OSCA
Version: 1.1.13
Command: chmod a+r OSCA -R && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data OSCA
StartedAt: 2021-01-15 10:31:06 -0500 (Fri, 15 Jan 2021)
EndedAt: 2021-01-15 10:31:30 -0500 (Fri, 15 Jan 2021)
EllapsedTime: 24.2 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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###
### Running command:
###
###   chmod a+r OSCA -R && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data OSCA
###
##############################################################################
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* checking for file 'OSCA/DESCRIPTION' ... OK
* preparing 'OSCA':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'stub.Rmd' using rmarkdown
--- finished re-building 'stub.Rmd'

cd book && "D:/biocbuild/bbs-3.13-bioc/R/bin/R" -e "bookdown::render_book('index.Rmd')"

R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> bookdown::render_book('index.Rmd')


processing file: index.Rmd

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output file: index.knit.md



processing file: installation.Rmd

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 $ echo   : logi FALSE
 $ results: chr "asis"


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output file: installation.knit.md



processing file: learning-r.Rmd

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output file: learning-r.knit.md



processing file: getting-datasets.Rmd

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label: unnamed-chunk-2
Loading required package: dbplyr
adding rname 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85241/suppl/GSE85241%5Fcellsystems%5Fdataset%5F4donors%5Fupdated%2Ecsv%2Egz'

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Quitting from lines 105-107 (getting-datasets.Rmd) 
Error in file(file, "rt") : cannot open the connection
Calls: local ... eval -> as.matrix -> read.delim -> read.table -> file
In addition: Warning messages:
1: In file.symlink(muraro.fname, local.name) :
  cannot symlink 'raw_data\1e3e06cde3c5a_GSE85241%255Fcellsystems%255Fdataset%255F4donors%255Fupdated%252Ecsv%252Egz' to 'GSE85241_cellsystems_dataset_4donors_updated.csv.gz', reason 'A required privilege is not held by the client'
2: In file(file, "rt") :
  cannot open file 'GSE85241_cellsystems_dataset_4donors_updated.csv.gz': No such file or directory

Execution halted
Error in Rscript_render(f, render_args, render_meta, add1, add2) : 
  Failed to compile getting-datasets.Rmd
Calls: <Anonymous> -> render_new_session -> Rscript_render
Execution halted
make: *** [Makefile:4: compiled] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted