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CHECK report for doseR on malbec2

This page was generated on 2019-04-09 11:52:45 -0400 (Tue, 09 Apr 2019).

Package 453/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
doseR 0.99.15
ake.vastermark
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/doseR
Branch: master
Last Commit: 5bf077d
Last Changed Date: 2019-03-05 12:00:00 -0400 (Tue, 05 Mar 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: doseR
Version: 0.99.15
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:doseR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings doseR_0.99.15.tar.gz
StartedAt: 2019-04-09 00:12:28 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:15:14 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 165.6 seconds
RetCode: 0
Status:  OK 
CheckDir: doseR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:doseR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings doseR_0.99.15.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/doseR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘0.99.15’
* 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:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL doseR
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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(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 
 10.099   0.316  10.407 

Example timings

doseR.Rcheck/doseR-Ex.timings

nameusersystemelapsed
dafs2.2730.0162.289
dafsFilter3.0490.0203.069
generateStats0.1510.0160.167
getLibsizes30.0940.0000.094
glSeq3.4100.0403.454
iqrxFilter0.1250.0000.125
make_RPKM0.1210.0040.125
plotExpr0.1480.0040.152
plotMA.se0.1590.0040.164
plotRatioBoxes0.1310.0000.131
plotRatioDensity0.1270.0040.130
quantFilter0.1020.0000.102
se.DM0.2750.0000.275
simpleFilter0.2920.0000.291
test_diffs0.1520.0000.152