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CHECK report for MSGFplus on merida1

This page was generated on 2019-04-16 11:58:00 -0400 (Tue, 16 Apr 2019).

Package 1007/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSGFplus 1.16.1
Thomas Lin Pedersen
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/MSGFplus
Branch: RELEASE_3_8
Last Commit: 62a4a5d
Last Changed Date: 2019-01-04 13:40:39 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MSGFplus
Version: 1.16.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSGFplus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSGFplus_1.16.1.tar.gz
StartedAt: 2019-04-16 01:27:15 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:28:00 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 45.2 seconds
RetCode: 0
Status:  OK 
CheckDir: MSGFplus.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSGFplus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSGFplus_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/MSGFplus.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.1’
* 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 ‘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 ... 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 ... 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/MSGFplus.Rcheck/00check.log’
for details.



Installation output

MSGFplus.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MSGFplus
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MSGFplus’ ...
** 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
* DONE (MSGFplus)

Tests output

MSGFplus.Rcheck/tests/test-all.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 169 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  1.755   0.184   1.919 

Example timings

MSGFplus.Rcheck/MSGFplus-Ex.timings

nameusersystemelapsed
chargeRange0.0030.0000.004
db0.0020.0000.002
enzyme0.0080.0020.010
fragmentation0.0050.0010.006
getMSGFpar0.0070.0010.009
instrument0.0070.0010.008
isotopeError0.0020.0000.003
lengthRange0.0030.0000.004
matches0.0030.0000.003
mods0.0030.0000.003
msgfAsync-class000
msgfPar-class0.0080.0010.009
msgfPar0.0240.0030.027
msgfParChargeRange-class0.0010.0010.001
msgfParEnzyme-class0.0030.0000.003
msgfParFragmentation-class0.0030.0010.003
msgfParFromID000
msgfParGUI000
msgfParInstrument-class0.0030.0000.003
msgfParIsotopeError-class0.0010.0000.001
msgfParLengthRange-class0.0000.0000.001
msgfParMatches-class000
msgfParModification-class0.0010.0010.001
msgfParModificationList-class0.0040.0000.004
msgfParNtt-class0.0000.0010.000
msgfParProtocol-class0.0030.0000.004
msgfParTda-class0.0010.0000.001
msgfParTolerance-class0.0010.0000.001
ntt0.0020.0010.003
protocol0.0070.0010.009
runMSGF0.0000.0010.001
tda0.0020.0000.002
tolerance0.0020.0000.003