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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:RforProteomics.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings RforProteomics_1.36.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-data-experiment/meat/RforProteomics.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘RforProteomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RforProteomics’ version ‘1.36.2’
* 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-3.16-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 loading without being on the library search path ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
    user system elapsed
id 6.841  0.193   7.033
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘RProtVis.Rmd’ using ‘UTF-8’... OK
  ‘RforProteomics.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘RProtVis.Rmd’ using rmarkdown
File figures/msanim1.gif not found in resource path
Error: processing vignette 'RProtVis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘RProtVis.Rmd’

--- re-building ‘RforProteomics.Rmd’ using rmarkdown
starting worker pid=1453474 on localhost:11663 at 12:15:16.277
starting worker pid=1453475 on localhost:11663 at 12:15:16.279
Loading required package: mzID
Loading required package: mzID
loaded mzID and set parent environment
loaded mzID and set parent environment
reading 55merge_omssa.mzid...
reading 55merge_tandem.mzid...
55merge_omssa.mzid DONE!
55merge_tandem.mzid DONE!
trying URL 'http://www.uniprot.org/uniprot/P00924.fasta'
Content type 'text/plain; format=fasta' length 562 bytes
==================================================
downloaded 562 bytes

--- finished re-building ‘RforProteomics.Rmd’

SUMMARY: processing the following file failed:
  ‘RProtVis.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.16-data-experiment/meat/RforProteomics.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL RforProteomics
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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)