##############################################################################
##############################################################################
###
### 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_1.33.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Repitools.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 ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ version ‘1.33.0’
* 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 use of PKG_*FLAGS in Makefiles ... 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 (user + system) or elapsed time > 5s
user system elapsed
methylEst 86.586 25.107 37.923
empBayes 44.128 15.829 27.035
BayMethList-class 11.772 1.019 12.818
sequenceCalc 10.653 1.552 12.228
cpgDensityCalc 10.430 1.546 12.037
determineOffset 7.155 1.031 8.208
maskOut 6.598 0.964 7.564
cpgDensityPlot 4.046 0.899 5.012
* 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-3.11-bioc/meat/Repitools.Rcheck/00check.log’
for details.
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.
> 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, 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
> 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
111.340 20.224 131.584
