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

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### Running command:
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###   /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
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* 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.

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

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 

name	user	system	elapsed
chargeRange	0.004	0.000	0.005
db	0.002	0.000	0.003
enzyme	0.011	0.000	0.011
fragmentation	0.004	0.003	0.008
getMSGFpar	0.009	0.000	0.010
instrument	0.007	0.000	0.006
isotopeError	0.002	0.000	0.003
lengthRange	0.003	0.000	0.002
matches	0.002	0.000	0.003
mods	0.005	0.000	0.005
msgfAsync-class	0.000	0.000	0.001
msgfPar-class	0.004	0.004	0.008
msgfPar	0.026	0.000	0.026
msgfParChargeRange-class	0.000	0.000	0.001
msgfParEnzyme-class	0.004	0.000	0.003
msgfParFragmentation-class	0.003	0.000	0.004
msgfParFromID	0	0	0
msgfParGUI	0	0	0
msgfParInstrument-class	0.004	0.000	0.004
msgfParIsotopeError-class	0.000	0.001	0.001
msgfParLengthRange-class	0.000	0.000	0.001
msgfParMatches-class	0	0	0
msgfParModification-class	0.002	0.000	0.002
msgfParModificationList-class	0.003	0.000	0.004
msgfParNtt-class	0	0	0
msgfParProtocol-class	0.004	0.000	0.004
msgfParTda-class	0.001	0.000	0.000
msgfParTolerance-class	0.001	0.000	0.001
ntt	0.000	0.002	0.002
protocol	0.006	0.000	0.006
runMSGF	0	0	0
tda	0.002	0.000	0.002
tolerance	0.003	0.000	0.003