##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:MSGFplus.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MSGFplus_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MSGFplus.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSGFplus/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSGFplus' version '1.26.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'MSGFplus' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/MSGFplus/man/msgfPar-class.Rd:121: missing link 'msgfParGUI'
  Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/MSGFplus/man/msgfPar-class.Rd:148: missing link 'msgfParGUI'
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MSGFplus.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 ... NOTE
Namespace in Imports field not imported from: 'ProtGenerics'
  All declared Imports should be used.
* 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 ... WARNING
Missing link or links in documentation object 'msgfPar-class.Rd':
  'msgfParGUI'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'test-all.R'
 OK
* 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: 2 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/MSGFplus.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch MSGFplus
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
* installing *source* package 'MSGFplus' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MSGFplus'
    finding HTML links ... done
    MSGFplus-package                        html  
    chargeRange                             html  
    db                                      html  
    enzyme                                  html  
    fragmentation                           html  
    getMSGFpar                              html  
    instrument                              html  
    isotopeError                            html  
    lengthRange                             html  
    matches                                 html  
    mods                                    html  
    msgfAsync-class                         html  
    msgfPar-class                           html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/MSGFplus/man/msgfPar-class.Rd:121: missing link 'msgfParGUI'
Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/meat/MSGFplus/man/msgfPar-class.Rd:148: missing link 'msgfParGUI'
    msgfPar                                 html  
    msgfParChargeRange-class                html  
    msgfParEnzyme-class                     html  
    msgfParFragmentation-class              html  
    msgfParFromID                           html  
    msgfParInstrument-class                 html  
    msgfParIsotopeError-class               html  
    msgfParLengthRange-class                html  
    msgfParMatches-class                    html  
    msgfParModification-class               html  
    msgfParModificationList-class           html  
    msgfParNtt-class                        html  
    msgfParProtocol-class                   html  
    msgfParTda-class                        html  
    msgfParTolerance-class                  html  
    ntt                                     html  
    protocol                                html  
    runMSGF                                 html  
    tda                                     html  
    tolerance                               html  
** 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 (MSGFplus)
Making 'packages.html' ... done

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
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.

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.

> library(testthat)
> test_check('MSGFplus')
Loading required package: MSGFplus

Attaching package: 'MSGFplus'

The following object is masked from 'package:testthat':

    matches

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 169 ]
> 
> proc.time()
   user  system elapsed 
   2.29    0.14    3.18