Package: doseR

Version: 1.3.0

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_1.3.0.tar.gz

StartedAt: 2020-01-16 03:56:38 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 04:01:39 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 301.3 seconds

RetCode: 0

Status:  OK

CheckDir: doseR.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/doseR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.3.0’
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL doseR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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 
 14.708   1.220  15.872 

name	user	system	elapsed
dafs	3.015	0.273	3.290
dafsFilter	3.300	0.265	3.571
generateStats	0.164	0.007	0.170
getLibsizes3	0.097	0.010	0.106
glSeq	4.097	0.123	4.221
iqrxFilter	0.160	0.007	0.168
make_RPKM	0.131	0.006	0.137
plotExpr	0.170	0.006	0.176
plotMA.se	0.137	0.011	0.150
plotRatioBoxes	0.168	0.009	0.178
plotRatioDensity	0.145	0.008	0.153
quantFilter	0.102	0.004	0.107
se.DM	0.374	0.005	0.380
simpleFilter	0.358	0.004	0.362
test_diffs	0.186	0.008	0.194