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CHECK report for MSGFplus on malbec2

This page was generated on 2019-10-16 12:05:25 -0400 (Wed, 16 Oct 2019).

Package 1052/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSGFplus 1.18.0
Thomas Lin Pedersen
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/MSGFplus
Branch: RELEASE_3_9
Last Commit: 159a2c3
Last Changed Date: 2019-05-02 11:53:49 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MSGFplus
Version: 1.18.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MSGFplus.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MSGFplus_1.18.0.tar.gz
StartedAt: 2019-10-16 03:22:51 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:23:34 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 42.9 seconds
RetCode: 0
Status:  OK 
CheckDir: MSGFplus.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MSGFplus.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MSGFplus_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MSGFplus.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.18.0’
* 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 ... 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/MSGFplus.Rcheck/00check.log’
for details.



Installation output

MSGFplus.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MSGFplus
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 169 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  1.909   0.097   2.021 

Example timings

MSGFplus.Rcheck/MSGFplus-Ex.timings

nameusersystemelapsed
chargeRange0.0040.0000.005
db0.0020.0000.003
enzyme0.0110.0000.011
fragmentation0.0040.0030.008
getMSGFpar0.0090.0000.010
instrument0.0070.0000.006
isotopeError0.0020.0000.003
lengthRange0.0030.0000.002
matches0.0020.0000.003
mods0.0050.0000.005
msgfAsync-class0.0000.0000.001
msgfPar-class0.0040.0040.008
msgfPar0.0260.0000.026
msgfParChargeRange-class0.0000.0000.001
msgfParEnzyme-class0.0040.0000.003
msgfParFragmentation-class0.0030.0000.004
msgfParFromID000
msgfParGUI000
msgfParInstrument-class0.0040.0000.004
msgfParIsotopeError-class0.0000.0010.001
msgfParLengthRange-class0.0000.0000.001
msgfParMatches-class000
msgfParModification-class0.0020.0000.002
msgfParModificationList-class0.0030.0000.004
msgfParNtt-class000
msgfParProtocol-class0.0040.0000.004
msgfParTda-class0.0010.0000.000
msgfParTolerance-class0.0010.0000.001
ntt0.0000.0020.002
protocol0.0060.0000.006
runMSGF000
tda0.0020.0000.002
tolerance0.0030.0000.003