Multiple platform build/check report for BioC 3.14 - CHECK results for MSGFplus on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: MSGFplus

Version: 1.28.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:MSGFplus.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MSGFplus_1.28.0.tar.gz

StartedAt: 2022-04-12 23:19:07 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 23:20:37 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 90.2 seconds

RetCode: 0

Status: WARNINGS

CheckDir: MSGFplus.Rcheck

Warnings: 2

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### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:MSGFplus.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MSGFplus_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MSGFplus.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.28.0'
* 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-3.14-bioc/meat/MSGFplus/man/msgfPar-class.Rd:121: missing link 'msgfParGUI'
  Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/meat/MSGFplus/man/msgfPar-class.Rd:148: missing link 'msgfParGUI'
  Warning: Package 'MSGFplus' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.14-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-3.14-bioc/meat/MSGFplus.Rcheck/00check.log'
for details.

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###
### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch MSGFplus
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* installing to library 'C:/Users/biocbuild/bbs-3.14-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-3.14-bioc/meat/MSGFplus/man/msgfPar-class.Rd:121: missing link 'msgfParGUI'
Rd warning: C:/Users/biocbuild/bbs-3.14-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
Warning: Package 'MSGFplus' is deprecated and will be removed from Bioconductor
  version 3.15
** testing if installed package can be loaded from final location
Warning: Package 'MSGFplus' is deprecated and will be removed from Bioconductor
  version 3.15
** testing if installed package keeps a record of temporary installation path
* DONE (MSGFplus)
Making 'packages.html' ... done


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 ]
Warning message:
Package 'MSGFplus' is deprecated and will be removed from Bioconductor
  version 3.15 
> 
> proc.time()
   user  system elapsed 
   3.29    0.15    4.21

name	user	system	elapsed
chargeRange	0	0	0
db	0	0	0
enzyme	0.01	0.00	0.01
fragmentation	0.02	0.00	0.02
getMSGFpar	0.02	0.00	0.01
instrument	0	0	0
isotopeError	0	0	0
lengthRange	0	0	0
matches	0	0	0
mods	0.02	0.00	0.01
msgfAsync-class	0	0	0
msgfPar-class	0	0	0
msgfPar	0.03	0.00	0.03
msgfParChargeRange-class	0	0	0
msgfParEnzyme-class	0	0	0
msgfParFragmentation-class	0	0	0
msgfParFromID	0	0	0
msgfParInstrument-class	0	0	0
msgfParIsotopeError-class	0	0	0
msgfParLengthRange-class	0	0	0
msgfParMatches-class	0	0	0
msgfParModification-class	0.02	0.00	0.02
msgfParModificationList-class	0	0	0
msgfParNtt-class	0	0	0
msgfParProtocol-class	0	0	0
msgfParTda-class	0.01	0.00	0.01
msgfParTolerance-class	0	0	0
ntt	0	0	0
protocol	0	0	0
runMSGF	0	0	0
tda	0	0	0
tolerance	0	0	0

CHECK results for MSGFplus on tokay2

Summary

Command output

Installation output

Tests output

Example timings