Package: pulsedSilac

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pulsedSilac.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pulsedSilac_1.0.1.tar.gz

StartedAt: 2020-04-15 04:49:17 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:54:03 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 285.2 seconds

RetCode: 0

Status:  OK

CheckDir: pulsedSilac.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pulsedSilac.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pulsedSilac_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/pulsedSilac.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pulsedSilac/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pulsedSilac’ version ‘1.0.1’
* package encoding: UTF-8
* 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 ‘pulsedSilac’ 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: OK

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘pulsedSilac’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
in method for ‘addMisscleavedPeptides’ with signature ‘"SilacProteinExperiment"’: no definition for class “SilacProteinExperiment”
in method for ‘addMisscleavedPeptides’ with signature ‘"SilacPeptideExperiment"’: no definition for class “SilacPeptideExperiment”
in method for ‘addMisscleavedPeptides’ with signature ‘"SilacProteomicsExperiment"’: no definition for class “SilacProteomicsExperiment”
** 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 (pulsedSilac)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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)
> library(pulsedSilac)
> 
> test_check("pulsedSilac")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 968 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 59.053   0.877  60.484 

name	user	system	elapsed
SilacPeptideExperiment-constructor	0.163	0.003	0.166
SilacProteinExperiment-constructor	0.025	0.001	0.025
SilacProteinPeptideExperiment-accessors	0.904	0.104	1.014
SilacProteomicsExperiment-accessors	1.175	0.085	1.264
SilacProteomicsExperiment-constructor	0.151	0.003	0.160
addMisscleavedPeptides	1.252	0.015	1.277
barplotCounts	1.335	0.007	1.360
barplotTimeCoverage	0.909	0.033	0.947
buildLinkerDf	0.006	0.001	0.007
calculateAIC	0.578	0.038	0.620
calculateIsotopeFraction	0.385	0.019	0.416
calculateIsotopeRatio	0.414	0.022	0.442
calculateOldIsotopePool	1.165	0.062	1.244
compareAIC	0.727	0.009	0.750
filterByMissingTimepoints	0.366	0.006	0.378
merge	0.739	0.010	0.767
mergeModelsLists	0.502	0.004	0.511
modelTurnover	0.424	0.003	0.429
mostStable	0.359	0.006	0.369
plotDistributionAssay	0.755	0.007	0.766
plotDistributionModel	0.765	0.006	0.774
plotIndividualModel	0.776	0.005	0.786
scatterCompareAssays	1.125	0.008	1.146
scatterCompareModels	0.676	0.008	0.691
upsetTimeCoverage	1.078	0.026	1.112