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CHECK report for QDNAseq on tokay2

This page was generated on 2019-10-16 12:29:26 -0400 (Wed, 16 Oct 2019).

Package 1284/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QDNAseq 1.20.0
Daoud Sie
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/QDNAseq
Branch: RELEASE_3_9
Last Commit: 88c420a
Last Changed Date: 2019-05-02 11:53:47 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS 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  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: QDNAseq
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QDNAseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings QDNAseq_1.20.0.tar.gz
StartedAt: 2019-10-16 06:15:19 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:20:25 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 306.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: QDNAseq.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QDNAseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings QDNAseq_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/QDNAseq.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'QDNAseq/DESCRIPTION' ... OK
* this is package 'QDNAseq' version '1.20.0'
* 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 'QDNAseq' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/applyFilters.Rd:31: file link 'madDiff' in package 'matrixStats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/binReadCounts.Rd:28: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/estimateCorrection.Rd:43: file link 'madDiff' in package 'matrixStats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/getBinAnnotations.Rd:43: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/highlightFilters.Rd:32: file link 'madDiff' in package 'matrixStats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/makeCgh.Rd:37: file link 'cghRaw' in package 'CGHbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/makeCgh.Rd:38: file link 'cghSeg' in package 'CGHbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/makeCgh.Rd:39: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/QDNAseq.Rcheck/00install.out' for details.
* 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 ... WARNING
Undocumented code objects:
  'exportVCF'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
callBins               18.25   0.11   18.36
frequencyPlot          17.38   0.08   17.45
normalizeSegmentedBins  8.64   0.03    8.67
segmentBins             7.78   0.03    7.82
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
frequencyPlot          16.43   0.01   16.45
callBins               15.32   0.11   15.42
normalizeSegmentedBins  5.31   0.03    5.34
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'QDNAseq,reproducibility.R'
  Running 'QDNAseq.R'
 OK
** running tests for arch 'x64' ...
  Running 'QDNAseq,reproducibility.R'
  Running 'QDNAseq.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: 2 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/QDNAseq.Rcheck/00check.log'
for details.



Installation output

QDNAseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/QDNAseq_1.20.0.tar.gz && rm -rf QDNAseq.buildbin-libdir && mkdir QDNAseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=QDNAseq.buildbin-libdir QDNAseq_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL QDNAseq_1.20.0.zip && rm QDNAseq_1.20.0.tar.gz QDNAseq_1.20.0.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  570k  100  570k    0     0  8157k      0 --:--:-- --:--:-- --:--:-- 9194k

install for i386

* installing *source* package 'QDNAseq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'QDNAseq'
    finding HTML links ... done
    LGG150                                  html  
    QDNAseq-defunct                         html  
    QDNAseq-package                         html  
    QDNAseqCopyNumbers                      html  
    QDNAseqReadCounts                       html  
    QDNAseqSignals                          html  
    addPhenodata                            html  
    applyFilters                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/applyFilters.Rd:31: file link 'madDiff' in package 'matrixStats' does not exist and so has been treated as a topic
    binReadCounts                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/binReadCounts.Rd:28: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
    callBins                                html  
    compareToReference                      html  
    correctBins                             html  
    createBins                              html  
    estimateCorrection                      html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/estimateCorrection.Rd:43: file link 'madDiff' in package 'matrixStats' does not exist and so has been treated as a topic
    exportBins                              html  
    finding level-2 HTML links ... done

    frequencyPlot                           html  
    getBinAnnotations                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/getBinAnnotations.Rd:43: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
    highlightFilters                        html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/highlightFilters.Rd:32: file link 'madDiff' in package 'matrixStats' does not exist and so has been treated as a topic
    isobarPlot                              html  
    makeCgh                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/makeCgh.Rd:37: file link 'cghRaw' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/makeCgh.Rd:38: file link 'cghSeg' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpyQnTy1/R.INSTALL1430419e3690/QDNAseq/man/makeCgh.Rd:39: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
    noisePlot                               html  
    normalizeBins                           html  
    normalizeSegmentedBins                  html  
    plot                                    html  
    poolRuns                                html  
    segmentBins                             html  
    smoothOutlierBins                       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 'QDNAseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QDNAseq' as QDNAseq_1.20.0.zip
* DONE (QDNAseq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'QDNAseq' successfully unpacked and MD5 sums checked

Tests output

QDNAseq.Rcheck/tests_i386/QDNAseq.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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("QDNAseq")
> 
> # Load data
> data(LGG150)
> data <- LGG150
> print(data)
QDNAseqReadCounts (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples 
  element names: counts 
protocolData: none
phenoData
  sampleNames: LGG150
  varLabels: name reads used.reads expected.variance
  varMetadata: labelDescription
featureData
  featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
    (38819 total)
  fvarLabels: chromosome start ... use (9 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> stopifnot(inherits(data, "QDNAseqReadCounts"))
> 
> # Plot isobars of read counts
> isobarPlot(data)
Plotting sample LGG150 median read counts
> 
> # Plot copy number profile
> plot(data, ylim=c(-100, 200))
Plotting sample LGG150 (1 of 1) ...
> highlightFilters(data, residual=TRUE, blacklist=TRUE)
Highlighted 3,375 bins.
> 
> # Filter out "bad" bins
> dataF <- applyFilters(data, residual=TRUE, blacklist=TRUE)
38,819	total bins
38,819	of which in selected chromosomes
36,722	of which with reference sequence
33,347	final bins
> print(dataF)
QDNAseqReadCounts (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples 
  element names: counts 
protocolData: none
phenoData
  sampleNames: LGG150
  varLabels: name reads used.reads expected.variance
  varMetadata: labelDescription
featureData
  featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
    (38819 total)
  fvarLabels: chromosome start ... use (9 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> plot(dataF, ylim=c(-100, 200))
Plotting sample LGG150 (1 of 1) ...
> stopifnot(inherits(dataF, "QDNAseqReadCounts"))
> 
> # Correct read counts as a function of GC content and mappability
> dataC <- correctBins(dataF)
Calculating correction for GC content and mappability
    Calculating fit for sample LGG150 (1 of 1) ...
Done.
> print(dataC)
QDNAseqCopyNumbers (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples 
  element names: copynumber 
protocolData: none
phenoData
  sampleNames: LGG150
  varLabels: name reads ... loess.family (6 total)
  varMetadata: labelDescription
featureData
  featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
    (38819 total)
  fvarLabels: chromosome start ... use (9 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> plot(dataC, ylim=c(-100, 200))
Plotting sample LGG150 (1 of 1) ...
> stopifnot(inherits(dataC, "QDNAseqCopyNumbers"))
> 
> # Normalize binned read counts to have diploid normal copy number
> dataN <- normalizeBins(dataC)
Applying median normalization ...
> print(dataN)
QDNAseqCopyNumbers (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples 
  element names: copynumber 
protocolData: none
phenoData
  sampleNames: LGG150
  varLabels: name reads ... loess.family (6 total)
  varMetadata: labelDescription
featureData
  featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
    (38819 total)
  fvarLabels: chromosome start ... use (9 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> plot(dataN)
Plotting sample LGG150 (1 of 1) ...
> stopifnot(inherits(dataN, "QDNAseqCopyNumbers"))
> 
> # Plot noise
> noisePlot(dataF)
Calculating correction for GC content and mappability
    Calculating fit for sample LGG150 (1 of 1) ...
Done.
> 
> # Segment copy numbers
> fit <- segmentBins(dataN)
Performing segmentation:
    Segmenting: LGG150 (1 of 1) ...
> print(fit)
QDNAseqCopyNumbers (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples 
  element names: copynumber, segmented 
protocolData: none
phenoData
  sampleNames: LGG150
  varLabels: name reads ... loess.family (6 total)
  varMetadata: labelDescription
featureData
  featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
    (38819 total)
  fvarLabels: chromosome start ... use (9 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> plot(fit)
Plotting sample LGG150 (1 of 1) ...
> stopifnot(inherits(fit, "QDNAseqCopyNumbers"))
> 
> # Call copy-number segments
> #fitC <- callBins(fit)
> #print(fitC)
> #plot(fitC)
> 
> proc.time()
   user  system elapsed 
  13.51    0.28   13.78 

QDNAseq.Rcheck/tests_x64/QDNAseq.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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("QDNAseq")
> 
> # Load data
> data(LGG150)
> data <- LGG150
> print(data)
QDNAseqReadCounts (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples 
  element names: counts 
protocolData: none
phenoData
  sampleNames: LGG150
  varLabels: name reads used.reads expected.variance
  varMetadata: labelDescription
featureData
  featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
    (38819 total)
  fvarLabels: chromosome start ... use (9 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> stopifnot(inherits(data, "QDNAseqReadCounts"))
> 
> # Plot isobars of read counts
> isobarPlot(data)
Plotting sample LGG150 median read counts
> 
> # Plot copy number profile
> plot(data, ylim=c(-100, 200))
Plotting sample LGG150 (1 of 1) ...
> highlightFilters(data, residual=TRUE, blacklist=TRUE)
Highlighted 3,375 bins.
> 
> # Filter out "bad" bins
> dataF <- applyFilters(data, residual=TRUE, blacklist=TRUE)
38,819	total bins
38,819	of which in selected chromosomes
36,722	of which with reference sequence
33,347	final bins
> print(dataF)
QDNAseqReadCounts (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples 
  element names: counts 
protocolData: none
phenoData
  sampleNames: LGG150
  varLabels: name reads used.reads expected.variance
  varMetadata: labelDescription
featureData
  featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
    (38819 total)
  fvarLabels: chromosome start ... use (9 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> plot(dataF, ylim=c(-100, 200))
Plotting sample LGG150 (1 of 1) ...
> stopifnot(inherits(dataF, "QDNAseqReadCounts"))
> 
> # Correct read counts as a function of GC content and mappability
> dataC <- correctBins(dataF)
Calculating correction for GC content and mappability
    Calculating fit for sample LGG150 (1 of 1) ...
Done.
> print(dataC)
QDNAseqCopyNumbers (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples 
  element names: copynumber 
protocolData: none
phenoData
  sampleNames: LGG150
  varLabels: name reads ... loess.family (6 total)
  varMetadata: labelDescription
featureData
  featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
    (38819 total)
  fvarLabels: chromosome start ... use (9 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> plot(dataC, ylim=c(-100, 200))
Plotting sample LGG150 (1 of 1) ...
> stopifnot(inherits(dataC, "QDNAseqCopyNumbers"))
> 
> # Normalize binned read counts to have diploid normal copy number
> dataN <- normalizeBins(dataC)
Applying median normalization ...
> print(dataN)
QDNAseqCopyNumbers (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples 
  element names: copynumber 
protocolData: none
phenoData
  sampleNames: LGG150
  varLabels: name reads ... loess.family (6 total)
  varMetadata: labelDescription
featureData
  featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
    (38819 total)
  fvarLabels: chromosome start ... use (9 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> plot(dataN)
Plotting sample LGG150 (1 of 1) ...
> stopifnot(inherits(dataN, "QDNAseqCopyNumbers"))
> 
> # Plot noise
> noisePlot(dataF)
Calculating correction for GC content and mappability
    Calculating fit for sample LGG150 (1 of 1) ...
Done.
> 
> # Segment copy numbers
> fit <- segmentBins(dataN)
Performing segmentation:
    Segmenting: LGG150 (1 of 1) ...
> print(fit)
QDNAseqCopyNumbers (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples 
  element names: copynumber, segmented 
protocolData: none
phenoData
  sampleNames: LGG150
  varLabels: name reads ... loess.family (6 total)
  varMetadata: labelDescription
featureData
  featureNames: 7:1-15000 7:15001-30000 ... 10:135525001-135534747
    (38819 total)
  fvarLabels: chromosome start ... use (9 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> plot(fit)
Plotting sample LGG150 (1 of 1) ...
> stopifnot(inherits(fit, "QDNAseqCopyNumbers"))
> 
> # Call copy-number segments
> #fitC <- callBins(fit)
> #print(fitC)
> #plot(fitC)
> 
> proc.time()
   user  system elapsed 
  10.81    0.25   11.04 

QDNAseq.Rcheck/tests_i386/QDNAseq,reproducibility.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> ######################################################################
> # This scripts asserts that for each processing step of QDNAseq
> # the output/results are reproducible (numerically equal).
> ######################################################################
> library("QDNAseq")
> 
> # Load data
> data(LGG150)
> data <- LGG150
> 
> # Filter out "bad" bins
> dataF <- applyFilters(data, residual=TRUE, blacklist=TRUE)
38,819	total bins
38,819	of which in selected chromosomes
36,722	of which with reference sequence
33,347	final bins
> dataFr <- applyFilters(data, residual=TRUE, blacklist=TRUE)
38,819	total bins
38,819	of which in selected chromosomes
36,722	of which with reference sequence
33,347	final bins
> stopifnot(all.equal(dataFr, dataF))
> 
> # Correct read counts as a function of GC content and mappability
> dataC <- correctBins(dataF)
Calculating correction for GC content and mappability
    Calculating fit for sample LGG150 (1 of 1) ...
Done.
> dataCr <- correctBins(dataF)
Calculating correction for GC content and mappability
    Calculating fit for sample LGG150 (1 of 1) ...
Done.
> stopifnot(all.equal(dataCr, dataC))
> 
> # Normalize binned read counts to have diploid normal copy number
> dataN <- normalizeBins(dataC)
Applying median normalization ...
> dataNr <- normalizeBins(dataC)
Applying median normalization ...
> stopifnot(all.equal(dataNr, dataN))
> 
> proc.time()
   user  system elapsed 
   6.76    0.31    7.06 

QDNAseq.Rcheck/tests_x64/QDNAseq,reproducibility.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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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.
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> ######################################################################
> # This scripts asserts that for each processing step of QDNAseq
> # the output/results are reproducible (numerically equal).
> ######################################################################
> library("QDNAseq")
> 
> # Load data
> data(LGG150)
> data <- LGG150
> 
> # Filter out "bad" bins
> dataF <- applyFilters(data, residual=TRUE, blacklist=TRUE)
38,819	total bins
38,819	of which in selected chromosomes
36,722	of which with reference sequence
33,347	final bins
> dataFr <- applyFilters(data, residual=TRUE, blacklist=TRUE)
38,819	total bins
38,819	of which in selected chromosomes
36,722	of which with reference sequence
33,347	final bins
> stopifnot(all.equal(dataFr, dataF))
> 
> # Correct read counts as a function of GC content and mappability
> dataC <- correctBins(dataF)
Calculating correction for GC content and mappability
    Calculating fit for sample LGG150 (1 of 1) ...
Done.
> dataCr <- correctBins(dataF)
Calculating correction for GC content and mappability
    Calculating fit for sample LGG150 (1 of 1) ...
Done.
> stopifnot(all.equal(dataCr, dataC))
> 
> # Normalize binned read counts to have diploid normal copy number
> dataN <- normalizeBins(dataC)
Applying median normalization ...
> dataNr <- normalizeBins(dataC)
Applying median normalization ...
> stopifnot(all.equal(dataNr, dataN))
> 
> proc.time()
   user  system elapsed 
   7.10    0.21    7.31 

Example timings

QDNAseq.Rcheck/examples_i386/QDNAseq-Ex.timings

nameusersystemelapsed
addPhenodata0.220.000.22
applyFilters0.290.020.31
binReadCounts000
callBins18.25 0.1118.36
compareToReference1.270.031.29
correctBins1.160.021.18
createBins000
estimateCorrection1.070.011.09
exportBins000
frequencyPlot17.38 0.0817.45
getBinAnnotations000
highlightFilters0.550.030.58
isobarPlot0.630.000.62
makeCgh0.950.000.95
noisePlot0.910.000.91
normalizeBins1.140.001.14
normalizeSegmentedBins8.640.038.67
plot1.720.001.72
poolRuns0.170.000.17
segmentBins7.780.037.82
smoothOutlierBins0.780.020.79

QDNAseq.Rcheck/examples_x64/QDNAseq-Ex.timings

nameusersystemelapsed
addPhenodata0.170.000.17
applyFilters0.200.000.21
binReadCounts000
callBins15.32 0.1115.42
compareToReference1.140.001.14
correctBins101
createBins000
estimateCorrection0.720.000.72
exportBins000
frequencyPlot16.43 0.0116.45
getBinAnnotations000
highlightFilters0.410.030.44
isobarPlot0.470.020.48
makeCgh0.780.000.78
noisePlot0.640.000.64
normalizeBins0.740.000.74
normalizeSegmentedBins5.310.035.34
plot1.120.001.13
poolRuns0.210.020.22
segmentBins4.750.004.75
smoothOutlierBins0.950.010.96