Jitao David Zhang
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/RTCA |
| Branch: RELEASE_3_9 |
| Last Commit: 4db9fac |
| Last Changed Date: 2019-05-02 11:53:12 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:47:43 -0400 (Wed, 16 Oct 2019).
| Package 1428/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RTCA 1.36.0 Jitao David Zhang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| 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 | |
| Package: RTCA |
| Version: 1.36.0 |
| 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_1.36.0.tar.gz |
| StartedAt: 2019-10-16 06:27:34 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:28:31 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 56.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RTCA.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/RTCA.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 ‘RTCA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RTCA’ version ‘1.36.0’ * 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
RTCA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RTCA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)
RTCA.Rcheck/tests/essentials.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(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: 2019-09-11 13:08:21
>
> tl2 <- addAction(tl, 1, "seeding")
> show(tl2)
RTCAtimeline
================================================
time action
0 start
1 seeding
================================================
Time unit: hour
RTCA-run start time: 2019-09-11 13:08:21
> 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: 2019-09-11 13:08:21
> rmAction(tl2, 1)
RTCAtimeline
================================================
time action
0 start
================================================
Time unit: hour
RTCA-run start time: 2019-09-11 13:08:21
> rmAction(tl2, -1)
RTCAtimeline
================================================
time action
0 start
1 seeding
================================================
Time unit: hour
RTCA-run start time: 2019-09-11 13:08:21
>
> updateAction(tl2, 1, "not seeding")
RTCAtimeline
================================================
time action
0 start
1 not seeding
================================================
Time unit: hour
RTCA-run start time: 2019-09-11 13:08:21
> updateAction(tl2, -1,"not seeding")
RTCAtimeline
================================================
time action
-1 not seeding
0 start
1 seeding
================================================
Time unit: hour
RTCA-run start time: 2019-09-11 13:08:21
> updateAction(tl2, -1,"not seeding", ifnotfound="ignore")
RTCAtimeline
================================================
time action
0 start
1 seeding
================================================
Time unit: hour
RTCA-run start time: 2019-09-11 13:08:21
> 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
3.291 0.381 3.619
RTCA.Rcheck/RTCA-Ex.timings
| name | user | system | elapsed | |
| RTCA-class | 0.383 | 0.054 | 0.438 | |
| RTCAtimeline-class | 0.003 | 0.000 | 0.003 | |
| alphaNames | 0.007 | 0.001 | 0.007 | |
| combineRTCA | 0.261 | 0.009 | 0.271 | |
| controlView | 0.243 | 0.009 | 0.252 | |
| derivativeTransform | 0.236 | 0.012 | 0.248 | |
| factor2numeric | 0.003 | 0.001 | 0.004 | |
| interpolationTransform | 0.324 | 0.040 | 0.364 | |
| nearestTimeIndex | 0.263 | 0.006 | 0.269 | |
| parseRTCA | 0.878 | 0.016 | 0.896 | |
| plateView | 0.392 | 0.006 | 0.398 | |
| plotGridEffect | 0.582 | 0.008 | 0.591 | |
| ratioTransform | 0.186 | 0.003 | 0.190 | |
| rgrTransform | 0.695 | 0.057 | 0.753 | |
| sliceRTCA | 0.205 | 0.015 | 0.221 | |
| smoothTransform | 0.392 | 0.007 | 0.400 | |
| spectramaxImport | 0.022 | 0.009 | 0.033 | |