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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1777/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCA 1.57.0  (landing page)
Jitao David Zhang
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/RTCA
git_branch: devel
git_last_commit: bd4a00f
git_last_commit_date: 2024-04-30 10:20:38 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for RTCA on palomino4

To the developers/maintainers of the RTCA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RTCA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: RTCA
Version: 1.57.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RTCA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RTCA_1.57.0.tar.gz
StartedAt: 2024-06-10 08:45:37 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 08:48:26 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 168.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RTCA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RTCA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RTCA_1.57.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/RTCA.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RTCA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTCA' version '1.57.0'
* 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 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 code 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 ... NOTE
checkRd: (-1) RTCA-class.Rd:79: Lost braces
    79 |     \item{expID}{code{signature(object = "RTCA")}: get Experiment ID}
       |                      ^
checkRd: (-1) RTCA-class.Rd:80: Lost braces
    80 |     \item{expID<-}{code{signature(object = "RTCA", value = "ANY")}: set Experiment ID}
       |                        ^
* 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 ... WARNING
Documented arguments not in \usage in Rd file 'interpolationTransform.Rd':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/RTCA.Rcheck/00check.log'
for details.


Installation output

RTCA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL RTCA
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

Attaching package: 'BiocGenerics'

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, aperm, 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, table, tapply,
    union, unique, unsplit, 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: 2024-05-06 15:28:07.324075 
> 
> tl2 <- addAction(tl, 1, "seeding")
> show(tl2)
RTCAtimeline
================================================
 time  action
    0   start
    1 seeding
================================================
Time unit: hour 
RTCA-run start time: 2024-05-06 15:28:07.324075 
> 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: 2024-05-06 15:28:07.324075 
> rmAction(tl2, 1)
RTCAtimeline
================================================
 time action
    0  start
================================================
Time unit: hour 
RTCA-run start time: 2024-05-06 15:28:07.324075 
> rmAction(tl2, -1)
RTCAtimeline
================================================
 time  action
    0   start
    1 seeding
================================================
Time unit: hour 
RTCA-run start time: 2024-05-06 15:28:07.324075 
> 
> updateAction(tl2, 1, "not seeding")
RTCAtimeline
================================================
 time      action
    0       start
    1 not seeding
================================================
Time unit: hour 
RTCA-run start time: 2024-05-06 15:28:07.324075 
> updateAction(tl2, -1,"not seeding")
RTCAtimeline
================================================
 time      action
   -1 not seeding
    0       start
    1     seeding
================================================
Time unit: hour 
RTCA-run start time: 2024-05-06 15:28:07.324075 
> updateAction(tl2, -1,"not seeding", ifnotfound="ignore")
RTCAtimeline
================================================
 time  action
    0   start
    1 seeding
================================================
Time unit: hour 
RTCA-run start time: 2024-05-06 15:28:07.324075 
> 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 
   1.79    3.96    5.70 

Example timings

RTCA.Rcheck/RTCA-Ex.timings

nameusersystemelapsed
RTCA-class0.360.040.39
RTCAtimeline-class000
alphaNames000
combineRTCA0.220.010.24
controlView0.110.030.14
derivativeTransform0.110.030.14
factor2numeric000
interpolationTransform0.160.030.20
nearestTimeIndex0.120.040.16
parseRTCA0.560.010.59
plateView0.270.000.28
plotGridEffect0.390.030.42
ratioTransform0.170.000.18
rgrTransform0.380.020.39
sliceRTCA0.140.030.17
smoothTransform0.230.000.23
spectramaxImport0.020.000.02