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CHECK report for QDNAseq on malbec2

This page was generated on 2019-10-16 12:04:08 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:QDNAseq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings QDNAseq_1.20.0.tar.gz
StartedAt: 2019-10-16 04:11:57 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:15:11 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 193.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: QDNAseq.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:QDNAseq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings QDNAseq_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/QDNAseq.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘QDNAseq’ 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
callBins               15.139  0.044  15.185
frequencyPlot          14.581  0.007  14.589
normalizeSegmentedBins  6.049  0.008   6.062
segmentBins             5.625  0.004   5.629
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/QDNAseq.Rcheck/00check.log’
for details.



Installation output

QDNAseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL QDNAseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘QDNAseq’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (QDNAseq)

Tests output

QDNAseq.Rcheck/tests/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-pc-linux-gnu (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.

> ######################################################################
> # 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 
  8.178   0.188   8.350 

QDNAseq.Rcheck/tests/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-pc-linux-gnu (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 
 11.152   0.256  11.393 

Example timings

QDNAseq.Rcheck/QDNAseq-Ex.timings

nameusersystemelapsed
addPhenodata0.2080.0040.212
applyFilters0.2830.0160.298
binReadCounts000
callBins15.139 0.04415.185
compareToReference1.1110.0001.111
correctBins0.9730.0000.973
createBins000
estimateCorrection0.7520.0000.753
exportBins000
frequencyPlot14.581 0.00714.589
getBinAnnotations000
highlightFilters0.7010.0110.713
isobarPlot0.4890.0120.501
makeCgh0.9040.0130.915
noisePlot0.6220.0070.630
normalizeBins1.0290.0041.032
normalizeSegmentedBins6.0490.0086.062
plot1.4960.0161.513
poolRuns0.2140.0070.222
segmentBins5.6250.0045.629
smoothOutlierBins0.6910.0000.693