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CHECK report for doseR on celaya2

This page was generated on 2019-10-16 13:04:22 -0400 (Wed, 16 Oct 2019).

Package 461/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
doseR 1.0.0
ake.vastermark
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/doseR
Branch: RELEASE_3_9
Last Commit: a59276b
Last Changed Date: 2019-05-02 11:54:14 -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: doseR
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:doseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings doseR_1.0.0.tar.gz
StartedAt: 2019-10-16 02:22:12 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:26:28 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 255.4 seconds
RetCode: 0
Status:  OK 
CheckDir: doseR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:doseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings doseR_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/doseR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘doseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘doseR’ version ‘1.0.0’
* 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 ‘doseR’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘1.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

doseR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL doseR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘doseR’ ...
** using staged installation
** R
** data
** 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 (doseR)

Tests output

doseR.Rcheck/tests/1.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-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(doseR)
> 
> data(hmel.se)
> f_se <- quantFilter(se, lo.bound = 0.4, hi.bound = 0.5)
Filtering removed 12660 (92.96%) of 13619 total loci.
> dm <- se.DM(f_se)
> temp <- glSeq(dm, "-1 + replicate")
> 
> RUnit::checkEqualsNumeric(round(temp@optinfo$val[4], 1), round(6.008, 1))
[1] TRUE
> RUnit::checkEqualsNumeric(round(temp@optinfo$val[5], 1), round(5.840, 1))
[1] TRUE
> 
> proc.time()
   user  system elapsed 
 13.385   1.125  14.459 

Example timings

doseR.Rcheck/doseR-Ex.timings

nameusersystemelapsed
dafs3.7360.3184.058
dafsFilter2.8450.2443.089
generateStats0.1690.0120.181
getLibsizes30.1070.0080.115
glSeq3.8540.1644.019
iqrxFilter0.1200.0040.124
make_RPKM0.1390.0070.145
plotExpr0.1980.0160.214
plotMA.se0.1260.0100.137
plotRatioBoxes0.0930.0050.099
plotRatioDensity0.1400.0120.153
quantFilter0.0720.0070.078
se.DM0.3790.0200.399
simpleFilter0.3430.0090.352
test_diffs0.1880.0070.195