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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DEqMS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings DEqMS_1.17.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DEqMS.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘DEqMS/DESCRIPTION’ ... OK
* this is package ‘DEqMS’ version ‘1.17.3’
* 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 ‘DEqMS’ can be installed ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... WARNING
Error in library(DEqMS, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘DEqMS’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘matrixStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Residualplot: no visible global function definition for ‘fitted’
Residualplot: no visible global function definition for ‘residuals’
VarianceScatterplot: no visible global function definition for ‘fitted’
peptideProfilePlot: no visible binding for global variable ‘variable’
peptideProfilePlot: no visible binding for global variable ‘value’
peptideProfilePlot: no visible binding for global variable ‘PSM_id’
peptideProfilePlot: no visible binding for global variable ‘Peptide’
spectraCounteBayes: no visible global function definition for ‘fitted’
Undefined global functions or variables:
  PSM_id Peptide fitted residuals value variable
Consider adding
  importFrom("stats", "fitted", "residuals")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘DEqMS-package-vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘DEqMS-package-vignette.Rmd’ using rmarkdown
trying URL 'https://ftp.ebi.ac.uk/pride-archive/2016/06/PXD004163/Yan_miR_Protein_table.flatprottable.txt'
Content type 'text/plain; charset=UTF-8' length 3515045 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/DEqMS.Rcheck/vign_test/DEqMS/vignettes/DEqMS-package-vignette_files/figure-html/boxplot1-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/DEqMS.Rcheck/vign_test/DEqMS/vignettes/DEqMS-package-vignette_files/figure-html/plot-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/DEqMS.Rcheck/vign_test/DEqMS/vignettes/DEqMS-package-vignette_files/figure-html/plot-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/DEqMS.Rcheck/vign_test/DEqMS/vignettes/DEqMS-package-vignette_files/figure-html/volcanoplot1-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/DEqMS.Rcheck/vign_test/DEqMS/vignettes/DEqMS-package-vignette_files/figure-html/volcanoplot2-1.png" but not available.
trying URL 'https://ftp.ebi.ac.uk/pride-archive/2014/09/PXD000279/proteomebenchmark.zip'
Content type 'application/zip' length 38428469 bytes (36.6 MB)
=========
downloaded 7.0 MB

Quitting from lines 227-230 (DEqMS-package-vignette.Rmd) 
Error: processing vignette 'DEqMS-package-vignette.Rmd' failed with diagnostics:
download from 'https://ftp.ebi.ac.uk/pride-archive/2014/09/PXD000279/proteomebenchmark.zip' failed
--- failed re-building ‘DEqMS-package-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘DEqMS-package-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/DEqMS.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL DEqMS
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘DEqMS’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DEqMS)