Multiple platform build/check report for BioC 3.9 experimental data - CHECK report for RforProteomics on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RforProteomics.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RforProteomics_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-data-experiment/meat/RforProteomics.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RforProteomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RforProteomics’ version ‘1.22.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RforProteomics’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘MSnbase::plot’ by ‘graphics::plot’ when loading ‘RforProteomics’
See ‘/home/biocbuild/bbs-3.9-data-experiment/meat/RforProteomics.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘RforProteomics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getThermoHelaPRTC
> ### Title: Dowload Thermo Hela PRTC data
> ### Aliases: getThermoHelaPRTC
> 
> ### ** Examples
> 
> getThermoHelaPRTC()
[1] "design.txt"                                 
[2] "swissprot_human_canonical_19_09_12.fasta.gz"
[3] "Thermo_Hela_PRTC_1.mgf.gz"                  
[4] "Thermo_Hela_PRTC_2.mgf.gz"                  
[5] "Thermo_Hela_PRTC_3.mgf.gz"                  
> getThermoHelaPRTC("design")
trying URL 'http://proteome.sysbiol.cam.ac.uk/lgatto/RforProteomics//design.txt'
Warning in download.file(src, destfile = dest, ...) :
  URL 'http://proteome.sysbiol.cam.ac.uk/lgatto/RforProteomics//design.txt': status was 'Couldn't connect to server'
Error in download.file(src, destfile = dest, ...) : 
  cannot open URL 'http://proteome.sysbiol.cam.ac.uk/lgatto/RforProteomics//design.txt'
Calls: getThermoHelaPRTC -> mapply ->  -> download.file
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.9-data-experiment/meat/RforProteomics.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL RforProteomics
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘RforProteomics’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘MSnbase::plot’ by ‘graphics::plot’ when loading ‘RforProteomics’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘MSnbase::plot’ by ‘graphics::plot’ when loading ‘RforProteomics’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘MSnbase::plot’ by ‘graphics::plot’ when loading ‘RforProteomics’
** testing if installed package keeps a record of temporary installation path
* DONE (RforProteomics)

CHECK report for RforProteomics on malbec2

Summary

Command output

Installation output

Tests output

Example timings