- using R Under development (unstable) (2019-12-07 r77541)
- using platform: x86_64-pc-linux-gnu (64-bit)
- using session charset: ISO8859-15
- checking for file 'dataone/DESCRIPTION' ... OK
- this is package 'dataone' version '2.1.2'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking serialization versions ... OK
- checking whether package 'dataone' can be installed ... OK
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking 'build' directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [16s/18s] OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking installed files from 'inst/doc' ... OK
- checking files in 'vignettes' ... OK
- checking examples ... ERROR
Running examples in 'dataone-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: listObjects
> ### Title: Retrieve the list of objects that match the search parameters
> ### Aliases: listObjects listObjects,D1Node-method
>
> ### ** Examples
>
> library(dataone)
> cn <- CNode("STAGING")
Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached: [cn-stage.test.dataone.org] Operation timed out after 10001 milliseconds with 0 out of 0 bytes received
Calls: CNode ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [38s/92s] OK
Running 'testthat.R' [38s/91s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in 'inst/doc' ... OK
- checking re-building of vignette outputs ... [33s/57s] WARNING
Error(s) in re-building vignettes:
...
--- re-building 'dataone-federation.Rmd' using rmarkdown
--- finished re-building 'dataone-federation.Rmd'
--- re-building 'dataone-overview.Rmd' using rmarkdown
Quitting from lines 63-72 (dataone-overview.Rmd)
Error: processing vignette 'dataone-overview.Rmd' failed with diagnostics:
Timeout was reached: [cn-stage.test.dataone.org] Operation timed out after 10001 milliseconds with 0 out of 0 bytes received
--- failed re-building 'dataone-overview.Rmd'
--- re-building 'download-data.Rmd' using rmarkdown
--- finished re-building 'download-data.Rmd'
--- re-building 'known-issues.Rmd' using rmarkdown
--- finished re-building 'known-issues.Rmd'
--- re-building 'searching-dataone.Rmd' using rmarkdown
--- finished re-building 'searching-dataone.Rmd'
--- re-building 'update-package.Rmd' using rmarkdown
--- finished re-building 'update-package.Rmd'
--- re-building 'upload-data.Rmd' using rmarkdown
--- finished re-building 'upload-data.Rmd'
SUMMARY: processing the following file failed:
'dataone-overview.Rmd'
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR, 1 WARNING