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CHECK report for RTCA on tokay1

This page was generated on 2020-04-15 12:18:58 -0400 (Wed, 15 Apr 2020).

Package 1488/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCA 1.38.0
Jitao David Zhang
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/RTCA
Branch: RELEASE_3_10
Last Commit: da8ffe5
Last Changed Date: 2019-10-29 13:08:07 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: RTCA
Version: 1.38.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCA.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings RTCA_1.38.0.tar.gz
StartedAt: 2020-04-15 06:19:10 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:20:04 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 53.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RTCA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCA.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings RTCA_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/RTCA.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RTCA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTCA' version '1.38.0'
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
Documented arguments not in \usage in documentation object 'interpolationTransform':
  '...'

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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'essentials.R'
 OK
** running tests for arch 'x64' ...
  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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/RTCA.Rcheck/00check.log'
for details.

Installation output

RTCA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/RTCA_1.38.0.tar.gz && rm -rf RTCA.buildbin-libdir && mkdir RTCA.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTCA.buildbin-libdir RTCA_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL RTCA_1.38.0.zip && rm RTCA_1.38.0.tar.gz RTCA_1.38.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 56905  100 56905    0     0  1004k      0 --:--:-- --:--:-- --:--:-- 1068k

install for i386

* installing *source* package 'RTCA' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RTCA'
    finding HTML links ... done
    RTCA-class                              html  
    finding level-2 HTML links ... done

    RTCAtimeline-class                      html  
    alphaNames                              html  
    combineRTCA                             html  
    controlView                             html  
    derivativeTransform                     html  
    factor2numeric                          html  
    interpolationTransform                  html  
    nearestTimeIndex                        html  
    parseRTCA                               html  
    plateView                               html  
    plotGridEffect                          html  
    ratioTransform                          html  
    rgrTransform                            html  
    sliceRTCA                               html  
    smoothTransform                         html  
    spectramaxImport                        html  
** 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

install for x64

* installing *source* package 'RTCA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTCA' as RTCA_1.38.0.zip
* DONE (RTCA)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'RTCA' successfully unpacked and MD5 sums checked

Tests output

RTCA.Rcheck/tests_i386/essentials.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 2020-03-11 12:59:55 
> 
> tl2 <- addAction(tl, 1, "seeding")
> show(tl2)
RTCAtimeline
================================================
 time  action
    0   start
    1 seeding
================================================
Time unit: hour 
RTCA-run start time: 2020-03-11 12:59:55 
> 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: 2020-03-11 12:59:55 
> rmAction(tl2, 1)
RTCAtimeline
================================================
 time action
    0  start
================================================
Time unit: hour 
RTCA-run start time: 2020-03-11 12:59:55 
> rmAction(tl2, -1)
RTCAtimeline
================================================
 time  action
    0   start
    1 seeding
================================================
Time unit: hour 
RTCA-run start time: 2020-03-11 12:59:55 
> 
> updateAction(tl2, 1, "not seeding")
RTCAtimeline
================================================
 time      action
    0       start
    1 not seeding
================================================
Time unit: hour 
RTCA-run start time: 2020-03-11 12:59:55 
> updateAction(tl2, -1,"not seeding")
RTCAtimeline
================================================
 time      action
   -1 not seeding
    0       start
    1     seeding
================================================
Time unit: hour 
RTCA-run start time: 2020-03-11 12:59:55 
> updateAction(tl2, -1,"not seeding", ifnotfound="ignore")
RTCAtimeline
================================================
 time  action
    0   start
    1 seeding
================================================
Time unit: hour 
RTCA-run start time: 2020-03-11 12:59:55 
> 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 
   2.04    0.12    2.34

RTCA.Rcheck/tests_x64/essentials.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: 2020-03-11 12:59:57 
> 
> tl2 <- addAction(tl, 1, "seeding")
> show(tl2)
RTCAtimeline
================================================
 time  action
    0   start
    1 seeding
================================================
Time unit: hour 
RTCA-run start time: 2020-03-11 12:59:57 
> 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: 2020-03-11 12:59:57 
> rmAction(tl2, 1)
RTCAtimeline
================================================
 time action
    0  start
================================================
Time unit: hour 
RTCA-run start time: 2020-03-11 12:59:57 
> rmAction(tl2, -1)
RTCAtimeline
================================================
 time  action
    0   start
    1 seeding
================================================
Time unit: hour 
RTCA-run start time: 2020-03-11 12:59:57 
> 
> updateAction(tl2, 1, "not seeding")
RTCAtimeline
================================================
 time      action
    0       start
    1 not seeding
================================================
Time unit: hour 
RTCA-run start time: 2020-03-11 12:59:57 
> updateAction(tl2, -1,"not seeding")
RTCAtimeline
================================================
 time      action
   -1 not seeding
    0       start
    1     seeding
================================================
Time unit: hour 
RTCA-run start time: 2020-03-11 12:59:57 
> updateAction(tl2, -1,"not seeding", ifnotfound="ignore")
RTCAtimeline
================================================
 time  action
    0   start
    1 seeding
================================================
Time unit: hour 
RTCA-run start time: 2020-03-11 12:59:57 
> 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 
   1.96    0.09    2.14

Example timings

RTCA.Rcheck/examples_i386/RTCA-Ex.timings

nameusersystemelapsed
RTCA-class0.160.000.17
RTCAtimeline-class000
alphaNames000
combineRTCA0.140.000.20
controlView0.180.000.31
derivativeTransform0.140.000.14
factor2numeric000
interpolationTransform0.170.030.21
nearestTimeIndex0.110.000.11
parseRTCA0.420.000.42
plateView0.20.00.2
plotGridEffect0.270.020.28
ratioTransform0.110.000.11
rgrTransform0.400.020.42
sliceRTCA0.110.000.11
smoothTransform0.250.000.25
spectramaxImport0.000.000.03

RTCA.Rcheck/examples_x64/RTCA-Ex.timings

nameusersystemelapsed
RTCA-class0.200.000.21
RTCAtimeline-class000
alphaNames000
combineRTCA0.140.020.16
controlView0.160.000.15
derivativeTransform0.140.000.14
factor2numeric0.010.000.02
interpolationTransform0.190.000.19
nearestTimeIndex0.140.000.14
parseRTCA0.740.010.75
plateView0.40.00.4
plotGridEffect0.490.000.49
ratioTransform0.110.000.11
rgrTransform0.40.00.4
sliceRTCA0.130.000.13
smoothTransform0.260.000.27
spectramaxImport0.020.000.01