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This page was generated on 2021-07-30 15:05:34 -0400 (Fri, 30 Jul 2021).

CHECK results for MSGFplus on nebbiolo1

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 1199/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSGFplus 1.26.0  (landing page)
Thomas Lin Pedersen
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/MSGFplus
Branch: RELEASE_3_13
Last Commit: c0c3ae3
Last Changed Date: 2021-05-19 12:08:05 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.26.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MSGFplus.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MSGFplus_1.26.0.tar.gz
StartedAt: 2021-07-29 10:46:56 -0400 (Thu, 29 Jul 2021)
EndedAt: 2021-07-29 10:47:27 -0400 (Thu, 29 Jul 2021)
EllapsedTime: 31.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MSGFplus.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MSGFplus.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MSGFplus_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/MSGFplus.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MSGFplus’ can be installed ... OK
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/MSGFplus.Rcheck/00check.log’
for details.



Installation output

MSGFplus.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MSGFplus
###
##############################################################################
##############################################################################


* installing to library ‘/home/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
** 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)

Tests output

MSGFplus.Rcheck/tests/test-all.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  2.046   0.147   2.164 

Example timings

MSGFplus.Rcheck/MSGFplus-Ex.timings

nameusersystemelapsed
chargeRange0.0020.0000.003
db0.0010.0000.002
enzyme0.0060.0000.006
fragmentation0.0000.0040.004
getMSGFpar0.0010.0040.004
instrument0.0030.0000.003
isotopeError0.0020.0000.001
lengthRange0.0000.0010.001
matches0.0000.0010.001
mods0.0030.0000.003
msgfAsync-class0.0000.0000.001
msgfPar-class0.0040.0000.005
msgfPar0.0140.0000.015
msgfParChargeRange-class0.0000.0000.001
msgfParEnzyme-class0.0000.0020.002
msgfParFragmentation-class0.0010.0010.002
msgfParFromID000
msgfParInstrument-class0.0020.0000.002
msgfParIsotopeError-class0.0000.0000.001
msgfParLengthRange-class0.0000.0000.001
msgfParMatches-class0.0010.0000.000
msgfParModification-class0.0020.0000.001
msgfParModificationList-class0.0020.0000.002
msgfParNtt-class000
msgfParProtocol-class0.0020.0000.002
msgfParTda-class0.0010.0000.000
msgfParTolerance-class000
ntt0.0000.0010.001
protocol0.0030.0000.003
runMSGF000
tda0.0010.0000.001
tolerance0.0020.0000.002