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This page was generated on 2021-11-29 15:05:30 -0500 (Mon, 29 Nov 2021).

CHECK results for MSGFplus on tokay2

To the developers/maintainers of the MSGFplus package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSGFplus.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1218/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSGFplus 1.28.0  (landing page)
Thomas Lin Pedersen
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/MSGFplus
git_branch: RELEASE_3_14
git_last_commit: d0bdc5b
git_last_commit_date: 2021-10-26 12:16:18 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  ERROR    ERROR  skippedskipped

Summary

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: 2021-11-29 01:36:23 -0500 (Mon, 29 Nov 2021)
EndedAt: 2021-11-29 01:37:43 -0500 (Mon, 29 Nov 2021)
EllapsedTime: 79.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MSGFplus.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running 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
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MSGFplus.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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.



Installation output

MSGFplus.Rcheck/00install.out

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch MSGFplus
###
##############################################################################
##############################################################################


* 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

Tests output

MSGFplus.Rcheck/tests/test-all.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 ]
Warning message:
Package 'MSGFplus' is deprecated and will be removed from Bioconductor
  version 3.15 
> 
> proc.time()
   user  system elapsed 
   2.43    0.09    3.29 

Example timings

MSGFplus.Rcheck/MSGFplus-Ex.timings

nameusersystemelapsed
chargeRange000
db000
enzyme0.020.000.02
fragmentation0.010.000.01
getMSGFpar000
instrument0.020.000.02
isotopeError000
lengthRange000
matches0.010.000.02
mods000
msgfAsync-class000
msgfPar-class0.020.000.01
msgfPar0.010.000.02
msgfParChargeRange-class000
msgfParEnzyme-class0.020.000.01
msgfParFragmentation-class000
msgfParFromID000
msgfParInstrument-class000
msgfParIsotopeError-class000
msgfParLengthRange-class000
msgfParMatches-class000
msgfParModification-class0.020.000.02
msgfParModificationList-class000
msgfParNtt-class000
msgfParProtocol-class000
msgfParTda-class000
msgfParTolerance-class000
ntt0.000.010.01
protocol000
runMSGF000
tda000
tolerance0.010.000.02