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CHECK report for RTCA on celaya2

This page was generated on 2020-01-16 13:32:10 -0500 (Thu, 16 Jan 2020).

Package 1483/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCA 1.39.0
Jitao David Zhang
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/RTCA
Branch: master
Last Commit: 8106b8a
Last Changed Date: 2019-10-29 13:35:07 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RTCA
Version: 1.39.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RTCA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RTCA_1.39.0.tar.gz
StartedAt: 2020-01-16 08:27:40 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 08:28:41 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 61.1 seconds
RetCode: 0
Status:  OK 
CheckDir: RTCA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RTCA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RTCA_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/RTCA.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 ‘RTCA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTCA’ version ‘1.39.0’
* 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 ‘RTCA’ 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘essentials.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

RTCA.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RTCA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘RTCA’ ...
** using staged installation
** R
** 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 (RTCA)

Tests output

RTCA.Rcheck/tests/essentials.Rout


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(RTCA)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RColorBrewer
Loading required package: gtools
> 
> 
> tl <- new("RTCAtimeline")
> timeUnit(tl) <- "hour"
> startTime(tl) <- Sys.time()-3e6
> show(tl)
RTCAtimeline
================================================
 time action
    0  start
================================================
Time unit: hour 
RTCA-run start time: 2019-12-12 15:08:31 
> 
> tl2 <- addAction(tl, 1, "seeding")
> show(tl2)
RTCAtimeline
================================================
 time  action
    0   start
    1 seeding
================================================
Time unit: hour 
RTCA-run start time: 2019-12-12 15:08:31 
> stopifnot(getAction(tl2, 0)=="start")
> stopifnot(is.null(getAction(tl2, -1)))
> 
> rmAction(tl2, 0)
RTCAtimeline
================================================
 time  action
    1 seeding
================================================
Time unit: hour 
RTCA-run start time: 2019-12-12 15:08:31 
> rmAction(tl2, 1)
RTCAtimeline
================================================
 time action
    0  start
================================================
Time unit: hour 
RTCA-run start time: 2019-12-12 15:08:31 
> rmAction(tl2, -1)
RTCAtimeline
================================================
 time  action
    0   start
    1 seeding
================================================
Time unit: hour 
RTCA-run start time: 2019-12-12 15:08:31 
> 
> updateAction(tl2, 1, "not seeding")
RTCAtimeline
================================================
 time      action
    0       start
    1 not seeding
================================================
Time unit: hour 
RTCA-run start time: 2019-12-12 15:08:31 
> updateAction(tl2, -1,"not seeding")
RTCAtimeline
================================================
 time      action
   -1 not seeding
    0       start
    1     seeding
================================================
Time unit: hour 
RTCA-run start time: 2019-12-12 15:08:31 
> updateAction(tl2, -1,"not seeding", ifnotfound="ignore")
RTCAtimeline
================================================
 time  action
    0   start
    1 seeding
================================================
Time unit: hour 
RTCA-run start time: 2019-12-12 15:08:31 
> startTime(tl2) <- as.POSIXct("2009-05-06 14:52:03")
> tl2
RTCAtimeline
================================================
 time  action
    0   start
    1 seeding
================================================
Time unit: hour 
RTCA-run start time: 2009-05-06 14:52:03 
> 
> ofile <- system.file("/extdata/testOutput.csv", package="RTCA")
> x <- parseRTCA(ofile)
Read 245 items
> 
> ## add actions to timeline
> x <- addAction(x, 22, "transfection")
> x <- addAction(x, 30, "change medium")
> 
> xr <- ratioTransform(x, 35)
> xrs <- smoothTransform(xr)
> xi <- interpolationTransform(x)
> xd <- derivativeTransform(x)
> xrgr <- rgrTransform(x)
> #plotRTCA(xrgr, xlim=c(35, 80), ylim=c(-0.2, 0.2))
> plot(sliceRTCA(x,0, 80)[,c(11,13)], type="l", col="black", ylim=c(0, 1.5))
> abline(h=0, col=2, lty=5)
> plot(sliceRTCA(xrgr, 20, 80)[,c(11,13)], type="l", col="black")
> abline(h=0, col=2, lty=5)
> 
> plotGridEffect(x)
> plotGridEffect(x, "col")
> plateView(sliceRTCA(x, 0, 80))
> 
> proc.time()
   user  system elapsed 
  3.409   0.400   3.756 

Example timings

RTCA.Rcheck/RTCA-Ex.timings

nameusersystemelapsed
RTCA-class0.4220.0520.474
RTCAtimeline-class0.0030.0010.004
alphaNames0.0080.0010.009
combineRTCA0.3210.0110.333
controlView0.2680.0080.276
derivativeTransform0.2200.0090.229
factor2numeric0.0010.0010.002
interpolationTransform0.2650.0310.295
nearestTimeIndex0.2790.0070.286
parseRTCA0.9340.0090.943
plateView0.3550.0030.358
plotGridEffect0.5900.0120.605
ratioTransform0.2500.0200.269
rgrTransform0.7070.0400.748
sliceRTCA0.2390.0020.240
smoothTransform0.5020.0270.529
spectramaxImport0.0260.0120.039