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CHECK report for pulsedSilac on malbec1

This page was generated on 2020-04-15 12:16:16 -0400 (Wed, 15 Apr 2020).

Package 1328/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pulsedSilac 1.0.1
Marc Pagès-Gallego
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/pulsedSilac
Branch: RELEASE_3_10
Last Commit: 43c451a
Last Changed Date: 2020-03-17 12:22:01 -0400 (Tue, 17 Mar 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  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: pulsedSilac
Version: 1.0.1
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:pulsedSilac.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings pulsedSilac_1.0.1.tar.gz
StartedAt: 2020-04-15 06:55:50 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 07:00:32 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 282.8 seconds
RetCode: 0
Status:  OK 
CheckDir: pulsedSilac.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:pulsedSilac.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings pulsedSilac_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/pulsedSilac.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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


Installation output

pulsedSilac.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL pulsedSilac
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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)

Tests output

pulsedSilac.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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)
> library(pulsedSilac)
> 
> test_check("pulsedSilac")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 968 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 55.916   0.612  56.730 

Example timings

pulsedSilac.Rcheck/pulsedSilac-Ex.timings

nameusersystemelapsed
SilacPeptideExperiment-constructor0.1920.0000.190
SilacProteinExperiment-constructor0.0320.0000.031
SilacProteinPeptideExperiment-accessors1.0040.1161.120
SilacProteomicsExperiment-accessors1.3920.0881.488
SilacProteomicsExperiment-constructor0.0960.0040.101
addMisscleavedPeptides1.4800.0641.549
barplotCounts1.6680.0521.726
barplotTimeCoverage0.9040.1081.035
buildLinkerDf0.0040.0000.005
calculateAIC0.6720.0360.706
calculateIsotopeFraction0.4520.0360.491
calculateIsotopeRatio0.3680.0560.424
calculateOldIsotopePool1.2800.0881.381
compareAIC0.7720.0440.819
filterByMissingTimepoints0.4040.0440.447
merge0.7520.0320.782
mergeModelsLists0.5520.0480.601
modelTurnover0.5760.0480.625
mostStable0.3920.0080.397
plotDistributionAssay0.9320.0520.986
plotDistributionModel0.8280.0280.857
plotIndividualModel0.7160.0440.760
scatterCompareAssays1.2040.0401.244
scatterCompareModels0.8080.0600.869
upsetTimeCoverage0.9600.0360.998