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CHECK report for Repitools on merida2

This page was generated on 2019-04-09 13:25:55 -0400 (Tue, 09 Apr 2019).

Package 1329/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Repitools 1.29.0
Mark Robinson
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/Repitools
Branch: master
Last Commit: 304dc7d
Last Changed Date: 2018-10-30 11:54:29 -0400 (Tue, 30 Oct 2018)
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  WARNINGS  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: Repitools
Version: 1.29.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Repitools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Repitools_1.29.0.tar.gz
StartedAt: 2019-04-09 03:16:15 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:25:11 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 536.0 seconds
RetCode: 0
Status:  OK 
CheckDir: Repitools.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Repitools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Repitools_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Repitools.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ version ‘1.29.0’
* 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 ‘Repitools’ 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 ... NOTE
.cpgBoxplots: no visible global function definition for ‘pdf’
.cpgBoxplots: no visible global function definition for ‘par’
.cpgBoxplots: no visible global function definition for ‘dev.off’
.diracBetaDirac: no visible global function definition for ‘dbeta’
.doBiasPlot: no visible global function definition for ‘plot’
.doBiasPlot: no visible global function definition for ‘lines’
.doBiasPlot: no visible global function definition for ‘lowess’
.doChrPlot: no visible global function definition for ‘plot’
.doChrPlot: no visible global function definition for ‘points’
.doChrPlot: no visible global function definition for ‘abline’
.drawSegs : <anonymous>: no visible global function definition for
  ‘lines’
.makeClusters : clusterScores: no visible global function definition
  for ‘embed’
.makeClusters : clusterScores: no visible global function definition
  for ‘filter’
.methylEstbeta: no visible global function definition for ‘qnorm’
.mydmarginal: no visible global function definition for ‘dbeta’
.mydmarginalDBD: no visible global function definition for ‘dbeta’
.plotFreqs: no visible global function definition for ‘layout’
.plotFreqs : <anonymous>: no visible global function definition for
  ‘matplot’
.plotFreqs : <anonymous>: no visible global function definition for
  ‘abline’
.plotFreqs : <anonymous>: no visible global function definition for
  ‘legend’
determineOffset: no visible global function definition for ‘par’
determineOffset: no visible global function definition for ‘grid’
determineOffset: no visible global function definition for ‘abline’
determineOffset: no visible global function definition for ‘text’
getSampleOffsets: no visible global function definition for ‘grid’
getSampleOffsets: no visible global function definition for ‘abline’
loadPairFile: no visible global function definition for ‘read.table’
plotQdnaByCN: no visible global function definition for ‘layout’
plotQdnaByCN: no visible global function definition for ‘grid’
plotQdnaByCN: no visible global function definition for ‘abline’
plotQdnaByCN: no visible global function definition for ‘plot’
processNDF: no visible global function definition for ‘read.table’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘nbrOfArrays’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘extract’
.blocksStats,AffymetrixCelSet-GRanges: no visible binding for global
  variable ‘verbose’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘getCdf’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘extractMatrix’
.blocksStats,GRangesList-GRanges: no visible global function definition
  for ‘p.adjust’
.blocksStats,matrix-GRanges: no visible global function definition for
  ‘t.test’
.blocksStats,matrix-GRanges: no visible global function definition for
  ‘pt’
.blocksStats,matrix-GRanges: no visible global function definition for
  ‘p.adjust’
.featureScores,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘getCdf’
.featureScores,AffymetrixCelSet-GRanges: no visible binding for global
  variable ‘verbose’
.featureScores,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘extractMatrix’
GCadjustCopy,GRanges-matrix-GCAdjustParams : <anonymous>: no visible
  global function definition for ‘lm’
GCadjustCopy,GRanges-matrix-GCAdjustParams : <anonymous>: no visible
  global function definition for ‘predict’
GCbiasPlots,AdjustedCopyEstimate: no visible global function definition
  for ‘par’
GCbiasPlots,AdjustedCopyEstimate : <anonymous>: no visible global
  function definition for ‘abline’
binPlots,ScoresList: no visible global function definition for ‘par’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘layout’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘par’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘matplot’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘plot.new’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘legend’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘mtext’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘axis’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘plot’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘plot.window’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘text’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘title’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘persp’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for ‘par’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for ‘matplot’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for ‘axis’
checkProbes,GRanges-GRanges : <anonymous> : <anonymous>: no visible
  global function definition for ‘matlines’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for ‘plot’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for ‘text’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for ‘mtext’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for ‘abline’
chromosomeCNplots,AdjustedCopyEstimate: no visible global function
  definition for ‘par’
chromosomeCNplots,CopyEstimate : <anonymous>: no visible global
  function definition for ‘str’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘layout’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘par’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘plot.new’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘legend’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘matplot’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘axis’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘mtext’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘par’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘layout’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘matplot’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘axis’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘mtext’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘title’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘plot.new’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘plot.window’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘text’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘bxp’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘rect’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘abline’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘plot’
clusterPlots,ScoresList: no visible global function definition for
  ‘kmeans’
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
  ‘Arguments’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘pushState’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘popState’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘nbrOfArrays’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘getCdf’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘getMainCdf’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘nbrOfUnits’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘indexOf’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘enter’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘getCellIndices’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘exit’
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
  ‘AromaCellSequenceFile’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘getChipType’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘countBases’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘extract’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘getNames’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘extractMatrix’
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
  ‘AromaCellCpgFile’
cpgBoxplots,matrix: no visible binding for global variable ‘Arguments’
cpgBoxplots,matrix: no visible global function definition for
  ‘pushState’
cpgBoxplots,matrix: no visible global function definition for
  ‘popState’
cpgBoxplots,matrix: no visible global function definition for ‘enter’
cpgBoxplots,matrix: no visible global function definition for ‘exit’
cpgDensityCalc,GRanges-BSgenome: no visible global function definition
  for ‘DNAString’
cpgDensityPlot,GRangesList: no visible global function definition for
  ‘rainbow’
cpgDensityPlot,GRangesList: no visible global function definition for
  ‘plot’
cpgDensityPlot,GRangesList: no visible global function definition for
  ‘lines’
cpgDensityPlot,GRangesList: no visible global function definition for
  ‘legend’
enrichmentPlot,GRangesList: no visible global function definition for
  ‘rainbow’
enrichmentPlot,GRangesList: no visible global function definition for
  ‘plot’
enrichmentPlot,GRangesList: no visible global function definition for
  ‘lines’
enrichmentPlot,GRangesList: no visible global function definition for
  ‘legend’
genQC,SequenceQCSet: no visible global function definition for
  ‘matplot’
genQC,SequenceQCSet: no visible global function definition for ‘legend’
genQC,SequenceQCSet: no visible global function definition for ‘par’
genQC,SequenceQCSet: no visible global function definition for ‘layout’
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for ‘par’
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for ‘matplot’
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for ‘abline’
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for ‘plot.new’
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for ‘legend’
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for ‘barplot’
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for ‘axis’
getProbePositionsDf,AffymetrixCdfFile: no visible global function
  definition for ‘getCellIndices’
getProbePositionsDf,AffymetrixCdfFile: no visible binding for global
  variable ‘AromaCellPositionFile’
getProbePositionsDf,AffymetrixCdfFile: no visible global function
  definition for ‘getChipType’
plotClusters,GRanges : <anonymous>: no visible global function
  definition for ‘par’
plotClusters,GRanges : <anonymous>: no visible global function
  definition for ‘plot’
plotClusters,GRanges : <anonymous>: no visible global function
  definition for ‘title’
plotClusters,GRanges : <anonymous>: no visible global function
  definition for ‘mtext’
plotClusters,GRanges : <anonymous>: no visible global function
  definition for ‘axis’
profilePlots,ScoresList: no visible global function definition for
  ‘rainbow’
profilePlots,ScoresList : <anonymous>: no visible global function
  definition for ‘matplot’
profilePlots,ScoresList : <anonymous>: no visible global function
  definition for ‘polygon’
profilePlots,ScoresList : <anonymous>: no visible global function
  definition for ‘legend’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘getCdf’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘getCellIndices’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘nbrOfArrays’
regionStats,AffymetrixCelSet: no visible binding for global variable
  ‘AromaCellPositionFile’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘getChipType’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘extract’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘extractMatrix’
sequenceCalc,GRanges-BSgenome : <anonymous>: no visible global function
  definition for ‘matchPattern’
writeWig,AffymetrixCelSet: no visible global function definition for
  ‘getNames’
writeWig,AffymetrixCelSet: no visible global function definition for
  ‘extract’
writeWig,AffymetrixCelSet: no visible global function definition for
  ‘getCdf’
writeWig,AffymetrixCelSet: no visible global function definition for
  ‘extractMatrix’
Undefined global functions or variables:
  Arguments AromaCellCpgFile AromaCellPositionFile
  AromaCellSequenceFile DNAString abline axis barplot bxp countBases
  dbeta dev.off embed enter exit extract extractMatrix filter getCdf
  getCellIndices getChipType getMainCdf getNames grid indexOf kmeans
  layout legend lines lm lowess matchPattern matlines matplot mtext
  nbrOfArrays nbrOfUnits p.adjust par pdf persp plot plot.new
  plot.window points polygon popState predict pt pushState qnorm
  rainbow read.table rect str t.test text title verbose
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow")
  importFrom("graphics", "abline", "axis", "barplot", "bxp", "grid",
             "layout", "legend", "lines", "matlines", "matplot", "mtext",
             "par", "persp", "plot", "plot.new", "plot.window", "points",
             "polygon", "rect", "text", "title")
  importFrom("stats", "dbeta", "embed", "filter", "kmeans", "lm",
             "lowess", "p.adjust", "predict", "pt", "qnorm", "t.test")
  importFrom("utils", "read.table", "str")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         75.274 13.066  27.913
empBayes          33.242  6.347  17.817
sequenceCalc       9.626  0.918  10.637
cpgDensityCalc     8.166  0.712  10.962
BayMethList-class  7.787  0.506   8.427
maskOut            4.658  0.462   5.242
determineOffset    4.568  0.534   8.251
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tests.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 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/Repitools.Rcheck/00check.log’
for details.



Installation output

Repitools.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Repitools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Repitools’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D R_NO_REMAP -I. -fPIC  -Wall -g -O2  -c const.c -o const.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D R_NO_REMAP -I. -fPIC  -Wall -g -O2  -c hyp2f1.c -o hyp2f1.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -D R_NO_REMAP -I. -fPIC  -Wall -g -O2  -c mtherr.c -o mtherr.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Repitools.so const.o hyp2f1.o mtherr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Repitools/libs
** 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
* DONE (Repitools)

Tests output

Repitools.Rcheck/tests/tests.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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.

> require("Repitools")
Loading required package: Repitools
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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

> require("BSgenome.Hsapiens.UCSC.hg18")
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer

Attaching package: 'rtracklayer'

The following object is masked from 'package:Repitools':

    blocks

> options(warn = -1)
> 
> probes <- data.frame(chr = c("chr1", "chr9", "chrY", "chr1", "chr21", "chr6", "chr6", "chr2", "chrX", "chr11"), position = c(10000, 5500, 100000, 11000, 20000000, 500100, 499900, 700000, 9900, 90000), strand = c('+', '+', '+', '+', '-', '-', '-', '+', '-', '+'), stringsAsFactors = FALSE)
> genes <- data.frame(chr = c("chr1", "chr9", "chr11", "chr1", "chr11", "chr6", "chr6", "chr22", "chrY", "chr21"), start = c(10000, 7900, 950000, 10500, 74000000, 450000, 5000000, 44000000, 1500, 9800000), end = c(12500, 9500, 1000000, 14500, 75000000, 500000, 9000000, 45000000, 3000, 10000000), strand = c('+', '-', '-', '+', '-', '-', '-', '+', '+', '-'), name = paste("Gene", 1:10), stringsAsFactors = FALSE)
> 
> crossMatch <- annotationLookup(probes, genes, 5000, 5000)
Processing mapping between probes and features.
Mapping done.
> correctCrossMatch <- list(indexes = list(`Gene 1` = as.integer(c(1, 4)), `Gene 2` = as.integer(2), `Gene 3` = integer(), `Gene 4` = as.integer(c(1, 4)), `Gene 5` = integer(), `Gene 6` = as.integer(c(6, 7)), `Gene 7` = integer(), `Gene 8` = integer(), `Gene 9` = integer(), `Gene 10` = integer()), offsets = list(`Gene 1` = as.integer(c(0, 1000)), `Gene 2` = as.integer(4000), `Gene 3` = numeric(), `Gene 4` = as.integer(c(-500, 500)), `Gene 5` = numeric(), `Gene 6` = as.integer(c(-100, 100)), `Gene 7` = numeric(), `Gene 8` = numeric(), `Gene 9` = numeric(), `Gene 10` = numeric()))
> names(correctCrossMatch$offsets$`Gene 1`) <- c(1, 4)
> names(correctCrossMatch$offsets$`Gene 2`) <- c(2)
> names(correctCrossMatch$offsets$`Gene 4`) <- c(1, 4)
> names(correctCrossMatch$offsets$`Gene 6`) <- c(6, 7)
> names(correctCrossMatch$offsets$`Gene 8`) <- character()
> names(correctCrossMatch$offsets$`Gene 9`) <- character()
> 
> if(!isTRUE(all.equal(crossMatch, correctCrossMatch))) 
+ 	stop("Error in annotationLookup function.")
> cat("anontationLookup tested fine.\n")
anontationLookup tested fine.
> 
> lookupTable <- makeWindowLookupTable(crossMatch$indexes, crossMatch$offsets, starts = seq(-5000, 4900, 100), ends = seq(-4900, 5000, 100))
> correctLookupTable <- matrix(NA, nrow = 10, ncol = 100, dimnames = list(genes$names, seq(-4950, 4950, 100)))
> correctLookupTable[1, c(50, 51)] <- 1
> correctLookupTable[1, c(60, 61)] <- 4
> correctLookupTable[2, c(90, 91)] <- 2
> correctLookupTable[4, c(45, 46)] <- 1
> correctLookupTable[4, c(55, 56)] <- 4
> correctLookupTable[6, c(49, 50)] <- 6
> correctLookupTable[6, c(51, 52)] <- 7
> 
> if(!all(lookupTable == correctLookupTable, na.rm = TRUE))
+     stop("Error in makeWindowLookupTable function")
> cat("makeWindowLookupTable tested fine.\n")
makeWindowLookupTable tested fine.
> 
> cpgDensity <- cpgDensityCalc(genes, organism = Hsapiens, window = 500, w.function="linear")
CpG density calculated for a sample.
> if(!isTRUE(all.equal(cpgDensity, c(5.784, 7.620, 5.828, 2.928, 2.080, 1.252, 0.000, 7.404, 3.928, 0.000))))
+     stop("cpgDensityCalc not working for window = 500, scaling = linear")
> cpgDensity <- cpgDensityCalc(genes, window = 100, w.function = "log", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(round(cpgDensity, 3), c(2.424, 1.882, 1.436, 0.084, 0.379, 0.000, 0.000, 0.263, 1.392, 0.000))))
+     stop("cpgDensityCalc not working for window = 100, scaling = log")
> cpgDensity <- cpgDensityCalc(genes, window = 1000, w.function = "exp", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(round(cpgDensity, 3), c(4.874, 5.835, 4.999, 2.239, 1.567, 0.851, 0.054, 5.589, 3.229,0.062))))
+     stop("cpgDensityCalc not working for window = 1000, scaling = exp")
> cpgDensity <- cpgDensityCalc(genes, window = 500, w.function = "none", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(cpgDensity, c(11, 14, 16, 6, 4, 2, 0, 15, 9, 0))))
+     stop("cpgDensityCalc not working for window = 500, scaling = none")
> cat("cpgDensityCalc tested fine.\n")
cpgDensityCalc tested fine.
> 
> GCpercent <- gcContentCalc(genes, Hsapiens, 500)
Calculating GC content.
> if(!isTRUE(all.equal(GCpercent, c(0.504, 0.586, 0.560, 0.470, 0.540, 0.304, 0.356, 0.638, 0.444, 0.388))))
+     stop("Error in gcContentCalc function")
> cat("gcContentCalc tested fine.\n")
gcContentCalc tested fine.
> 
> findsCount <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT")
> if(!isTRUE(all.equal(findsCount, c(1, 1, 0, 2, 1, 8, 2, 0, 4, 10))))
+     stop("Error in sequenceCalc function counting task")
> 
> findsPlaces <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT", positions = TRUE)
> correctPlaces <- list(-62, 181, NULL, c(-140, -98), 231, c(-219, -146, -88, -12, 12, 182, 209, 214), c(-61, 60), NULL, c(-115, -30, 11, 80), c(-238, -228, -202, -189, -177, -106, -21, 148, 158, 238))
> if(!isTRUE(all.equal(findsPlaces, correctPlaces)))
+     stop("Error in sequenceCalc function positions task")
> cat("sequenceCalc tested fine.\n")
sequenceCalc tested fine.
> cat("All tests passed.\n")
All tests passed.
> 
> proc.time()
   user  system elapsed 
 97.708  10.644 109.336 

Example timings

Repitools.Rcheck/Repitools-Ex.timings

nameusersystemelapsed
BAM2GRanges0.1610.0050.167
BayMethList-class7.7870.5068.427
GCadjustCopy0.0000.0000.042
GCbiasPlots0.0010.0000.001
QdnaData0.0870.0040.091
abcdDNA000
absoluteCN0.0010.0000.000
annoDF2GR0.0170.0000.017
annoGR2DF0.1180.0040.139
annotationBlocksCounts0.1390.0030.142
annotationBlocksLookup0.0500.0000.051
annotationCounts0.1190.0030.122
annotationLookup0.0960.0010.097
binPlots2.2000.2852.819
blocksStats0.1630.0030.167
checkProbes0.1100.0020.344
chromosomeCNplots0.0010.0010.000
clusterPlots0.8160.1091.411
cpgDensityCalc 8.166 0.71210.962
cpgDensityPlot3.4860.5594.166
determineOffset4.5680.5348.251
empBayes33.242 6.34717.817
enrichmentCalc1.5000.2721.826
enrichmentPlot1.4110.3432.013
featureBlocks0.0260.0000.028
featureScores0.6590.1010.825
findClusters2.0640.1512.584
gcContentCalc3.8510.4394.318
genQC0.000.000.06
genomeBlocks0.0900.0000.091
getProbePositionsDf0.0000.0010.000
getSampleOffsets0.0000.0000.001
hyper0.0010.0000.001
loadPairFile0.0000.0000.001
loadSampleDirectory000
makeWindowLookupTable0.0590.0010.059
mappabilityCalc000
maskOut4.6580.4625.242
mergeReplicates1.0120.0421.062
methylEst75.27413.06627.913
multiHeatmap0.0470.0020.049
plotClusters0.1410.0040.148
plotQdnaByCN0.0000.0000.001
processNDF0.0000.0010.000
profilePlots000
regionStats0.0000.0000.001
relativeCN0.0780.0020.079
sequenceCalc 9.626 0.91810.637
setCNVOffsets000
summarizeScores0.7480.1170.876
writeWig000