henrikbengtsson / aroma.core Goto Github PK

aroma.core:
R/AbstractCNData.R:    if (is.data.frame(chromosome)) {
R/AbstractCNData.R:  as.data.frame(this)
R/AbstractCNData.R:  data <- as.data.frame(this, ...)
R/AbstractCNData.R:  data <- as.data.frame(this, ...)
R/AbstractPSCNData.R:    if (is.data.frame(chromosome)) {
R/AbstractPSCNData.R:  data <- as.data.frame(this)
R/AromaTabularBinaryFile.R:  if (is.data.frame(values) || is.matrix(values)) {
R/AromaTabularBinaryFile.R:    if (is.data.frame(values) || is.matrix(values)) {
R/ChromosomalModel.drawCytoband.R:  labelChr <- data.frame(chromosome=chromosome)
R/CopyNumberOutliers.R:setMethodS3("as.data.frame", "CopyNumberOutliers", function(x, ...) {
R/CopyNumberOutliers.R:  data <- as.data.frame(this)
R/CopyNumberOutliers.R:  data <- as.data.frame(this)
R/CopyNumberRegions.EXT2.R:  data <- as.data.frame(this)
R/CopyNumberRegions.EXT2.R:  data <- as.data.frame(this)
R/CopyNumberRegions.EXT.R:  df <- as.data.frame(this)
R/CopyNumberRegions.EXT.R:  data <- as.data.frame(this)
R/CopyNumberRegions.EXT.R:  dfList <- lapply(regList, FUN=as.data.frame)
R/CopyNumberRegions.EXT.R:  data <- as.data.frame(this)
R/CopyNumberRegions.R:setMethodS3("as.data.frame", "CopyNumberRegions", function(x, ...) {
R/CopyNumberRegions.R:  data <- as.data.frame(data)
R/CopyNumberRegions.R:  data <- as.data.frame(this, ...)
R/CopyNumberRegions.R:  dfThis <- as.data.frame(this)
R/CopyNumberRegions.R:  dfOther <- as.data.frame(other)
R/CopyNumberRegions.R:  data <- as.data.frame(this)
R/CopyNumberRegions.R:  data <- as.data.frame(this)
R/CopyNumberRegions.R:  data <- as.data.frame(this)
R/CopyNumberSegmentationModel.R:          df0 <- as.data.frame(cnr)
R/drawCytoband2.R:  info <- data.frame(Color=color, ColorName=I(pal))
R/GLAD.EXTS.R:  LabelChr <- data.frame(Chromosome=chromosome)
R/NonPairedPSCNData.R:    if (is.data.frame(chromosome)) {
R/NonPairedPSCNData.R:setMethodS3("as.NonPairedPSCNData", "data.frame", function(this, ...) {
R/NonPairedPSCNData.R:  data <- as.data.frame(this)
R/NonPairedPSCNData.R:  data <- as.data.frame(this)
R/PairedPSCNData.PLOT.R:  data <- as.data.frame(this)
R/PairedPSCNData.R:    if (is.data.frame(chromosome)) {
R/PairedPSCNData.R:setMethodS3("as.PairedPSCNData", "data.frame", function(this, ...) {
R/PairedPSCNData.R:  dataT <- as.data.frame(T)
R/PairedPSCNData.R:  dataN <- as.data.frame(N)
R/PairedPSCNData.R:  data <- as.data.frame(this)
R/PairedPSCNData.R:  data <- as.data.frame(this)
R/PairedPSCNData.R:  data <- as.data.frame(CT)
R/PairedPSCNData.R:  data <- as.data.frame(CT)
R/profileCGH.plotProfile2.R:  LabelChr <- data.frame(Chromosome=chromosome)
R/profileCGH.plotProfile2.R:    if (is.data.frame(fit$BkpInfo)) {
R/RawGenomicSignals.R:    regions <- as.data.frame(regions)
R/RawGenomicSignals.R:    regions <- as.data.frame(regions)
R/RawGenomicSignals.R:  if (!is.data.frame(regions)) {
R/RawGenomicSignals.R:    throw("Argument 'regions' is neither a CopyNumberRegions object, a data.frame, nor a matrix: ", cl)
R/RawGenomicSignals.R:    regions <- cbind(data.frame(chromosome=chromosomes), regions)
R/RawGenomicSignals.R:setMethodS3("as.data.frame", "RawGenomicSignals", function(x, ..., sort=FALSE) {
R/RawGenomicSignals.R:  NextMethod("as.data.frame")
R/RawGenomicSignals.R:    data <- as.data.frame(data, virtual=FALSE)
R/RawGenomicSignals.R:  data <- as.data.frame(this, ...)
R/RawGenomicSignals.R:  dataY <- as.data.frame(this)
R/RawGenomicSignals.R:  data <- as.data.frame(this)
R/RawGenomicSignals.R:  dataOut <- as.data.frame(res)
R/RawGenomicSignals.R:    YsSS <- as.data.frame(resSS)[,fields, drop=FALSE]
R/RawGenomicSignals.segmentByCBS.R:  cnrData <- as.data.frame(cnr)
R/RawGenomicSignals.segmentByGLAD.R:  cnData <- data.frame(
R/RawGenomicSignals.segmentByGLAD.R:  cnrData <- as.data.frame(cnr)
R/RawGenomicSignals.segmentByHaarSeg.R:  cnrData <- as.data.frame(cnr)
R/RawGenomicSignals.SEG.R:  data <- as.data.frame(this, translate=FALSE)
R/RawSequenceReads.EXTRAS.R:         dataChecksum=getChecksum(as.data.frame(rsr)), by=by, region=region)
R/RichDataFrame.R:  data <- data.frame(...)
R/RichDataFrame.R:  data <- as.data.frame(data)
R/RichDataFrame.R:  print(as.data.frame(x, ...))
R/RichDataFrame.R:  data <- as.data.frame(this)
R/RichDataFrame.R:setMethodS3("as.data.frame", "RichDataFrame", function(x, ..., virtual=TRUE, translate=TRUE) {
R/RichDataFrame.R:  class(data) <- "data.frame"
R/RichDataFrame.R:  x <- as.data.frame(x)
R/RichDataFrame.R:  class(res) <- "data.frame"
R/RichDataFrame.R:    data <- as.data.frame(this, virtual=FALSE)
R/RichDataFrame.R:  class(this) <- "data.frame"
R/RichDataFrame.R:  class(other) <- "data.frame"
R/SegmentedGenomicSignalsInterface.R:setMethodS3("as.data.frame", "SegmentedGenomicSignalsInterface", function(x, ..., virtual=TRUE) {
R/SegmentedGenomicSignalsInterface.R:    df <- NextMethod("as.data.frame", virtual=virtual)
R/SegmentedGenomicSignalsInterface.R:    df <- NextMethod("as.data.frame")
tests/mergeBoxplotStats.R:x <- as.data.frame(x)
tests/PairedPSCNData.R:verbose && print(verbose, head(as.data.frame(data)));
tests/PairedPSCNData.R:verbose && print(verbose, head(as.data.frame(dataN)));
tests/PairedPSCNData.R:verbose && print(verbose, head(as.data.frame(data)));
tests/PairedPSCNData.R:verbose && print(verbose, head(as.data.frame(data)));
tests/PairedPSCNData.R:verbose && print(verbose, head(as.data.frame(data)));
tests/PairedPSCNData.R:verbose && print(verbose, head(as.data.frame(data)));
tests/PairedPSCNData,SEG.R:verbose && print(verbose, head(as.data.frame(data)));
tests/PairedPSCNData,SEG.R:verbose && print(verbose, head(as.data.frame(data)));
tests/PairedPSCNData,SEG.R:print(head(as.data.frame(fit)));
tests/PairedPSCNData,SEG.R:print(head(as.data.frame(fit)));
tests/RawGenomicSignals.R:regions <- data.frame(
tests/RichDataFrame.R:data <- as.data.frame(cn)
tests/RichDataFrame.R:dataSb <- as.data.frame(cnSb)

About to run xvfb-run R CMD check aroma.core_3.3.0.tar.gz
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://cloud.r-project.org
* using log directory ‘/home/docker/aroma.core.Rcheck’
* using R Under development (unstable) (2022-11-09 r83320)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘aroma.core/DESCRIPTION’ ... OK
* this is package ‘aroma.core’ version ‘3.3.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking: 'EBImage', 'GLAD'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘aroma.core’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 loading without being on the library search path ... 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 ... NOTE
Package unavailable to check Rd xrefs: ‘GLAD’
* 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 examples ... ERROR
Running examples in ‘aroma.core-Ex.R’ failed
The error most likely occurred in:
> ### Name: segmentByMPCBS.RawGenomicSignals
> ### Title: Segment copy numbers using the multi-platform CBS (mpCBS) method
> ### Aliases: segmentByMPCBS.RawGenomicSignals
> ### RawGenomicSignals.segmentByMPCBS
> ### segmentByMPCBS,RawGenomicSignals-method
> ### Keywords: internal methods IO
>
> ### ** Examples
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Simulating copy-number data from multiple platforms
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Piecewise-constant copy-number state function
> cnState <- function(x, ...) {
+ n <- length(x)
+ mu <- double(n)
+ mu[20e6 <= x & x <= 30e6] <- +1
+ mu[65e6 <= x & x <= 80e6] <- -1
+ mu
+ } # cnState()
>
> xMax <- 100e6
>
> Js <- c(200, 400, 100)
> bs <- c(1, 1.4, 0.5)
> as <- c(0, +0.5, -0.5)
> sds <- c(0.5, 0.3, 0.8)
>
> cnList <- list()
> for (kk in seq_along(Js)) {
+ J <- Js[kk]
+ a <- as[kk]
+ b <- bs[kk]
+ sd <- sds[kk]
+ x <- sort(runif(J, max=xMax))
+ mu <- a + b * cnState(x)
+ eps <- rnorm(J, sd=sd)
+ y <- mu + eps
+ cn <- RawCopyNumbers(y, x)
+ cnList[[kk]] <- cn
+ }
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Merge platform data (record their sources in 'id')
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cn <- Reduce(append, cnList)
> plot(cn, ylim=c(-3,3), col=cn$id)
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Segment
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> legend <- c()
>
> if (require("DNAcopy")) {
+ fit <- segmentByCBS(cn)
+ cnr <- extractCopyNumberRegions(fit)
+ print(cnr)
+ drawLevels(cnr, col="white", lwd=6)
+ drawLevels(cnr, col="red", lwd=3)
+ legend <- c(legend, red="CBS")
+ }
Loading required package: DNAcopy
CopyNumberRegions:
Number of regions: 5
>
>
> if (require("mpcbs")) {
+ fit <- local({
+ ## WORKAROUND: There's a _R_CHECK_LENGTH_1_LOGIC2_ bug in
+ ## mpcbs::mpcbs.mbic(). Until fixed, we need to disable this check
+ ## while calling segmentByMPCBS().
+ ovalue <- Sys.getenv("_R_CHECK_LENGTH_1_LOGIC2_")
+ on.exit(Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_"=ovalue))
+ ovalue <- Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_"="warn,verbose")
+ segmentByMPCBS(cn)
+ })
+ cnr <- extractCopyNumberRegions(fit)
+ print(cnr)
+ drawLevels(cnr, col="white", lwd=6)
+ drawLevels(cnr, col="blue", lwd=3)
+ legend <- c(legend, blue="MPCBS")
+ }
Loading required package: mpcbs
Loading required package: fields
Loading required package: spam
Spam version 2.9-1 (2022-08-07) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: ‘spam’
The following object is masked from ‘package:aroma.core’:
display
The following object is masked from ‘package:R.utils’:
cleanup
The following objects are masked from ‘package:base’:
backsolve, forwardsolve
Loading required package: viridis
Loading required package: viridisLite
Try help(fields) to get started.
Error in is.na(rratio) || (length(rratio) != K) :
'length = 3' in coercion to 'logical(1)'
Calls: local ... system.time -> do.call -> mpcbs.mbic -> fcompute.max.ProjectedZ
Timing stopped at: 0 0 0.001
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘PairedPSCNData,SEG.R’
Running ‘PairedPSCNData.R’
Running ‘RawCopyNumbers,states.R’
Running ‘RawCopyNumbers.R’
Running ‘RawGenomicSignals.R’
Running ‘RawGenomicSignals.SEG,MP.R’
ERROR
Running the tests in ‘tests/RawGenomicSignals.SEG,MP.R’ failed.
Last 13 lines of output:
cleanup

The following objects are masked from 'package:base':

backsolve, forwardsolve

Loading required package: viridis
Loading required package: viridisLite

Try help(fields) to get started.
Error in is.na(rratio) || (length(rratio) != K) :
'length = 3' in coercion to 'logical(1)'
Calls: local ... system.time -> do.call -> mpcbs.mbic -> fcompute.max.ProjectedZ
Timing stopped at: 0 0 0.001
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See ‘/home/docker/aroma.core.Rcheck/00check.log’ for details.