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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:52:50 -0400 (Wed, 16 Oct 2019).
| Package 1284/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| QDNAseq 1.20.0 Daoud Sie
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: QDNAseq |
| Version: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:QDNAseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings QDNAseq_1.20.0.tar.gz |
| StartedAt: 2019-10-16 05:52:44 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:57:17 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 272.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: QDNAseq.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:QDNAseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings QDNAseq_1.20.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/QDNAseq.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 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
callBins 19.186 0.491 19.686
frequencyPlot 18.750 0.498 19.254
normalizeSegmentedBins 6.156 0.256 6.415
segmentBins 5.979 0.181 6.162
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/QDNAseq.Rcheck/00check.log’
for details.
QDNAseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL QDNAseq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)
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-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.
> ######################################################################
> # 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
9.562 0.883 10.399
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-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.
> 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
15.550 1.287 16.801
QDNAseq.Rcheck/QDNAseq-Ex.timings
| name | user | system | elapsed | |
| addPhenodata | 0.215 | 0.028 | 0.243 | |
| applyFilters | 0.309 | 0.034 | 0.344 | |
| binReadCounts | 0.000 | 0.000 | 0.001 | |
| callBins | 19.186 | 0.491 | 19.686 | |
| compareToReference | 1.093 | 0.150 | 1.243 | |
| correctBins | 0.896 | 0.101 | 0.998 | |
| createBins | 0.000 | 0.000 | 0.001 | |
| estimateCorrection | 0.873 | 0.078 | 0.951 | |
| exportBins | 0.000 | 0.000 | 0.001 | |
| frequencyPlot | 18.750 | 0.498 | 19.254 | |
| getBinAnnotations | 0.000 | 0.001 | 0.000 | |
| highlightFilters | 0.558 | 0.119 | 0.679 | |
| isobarPlot | 0.758 | 0.043 | 0.802 | |
| makeCgh | 1.015 | 0.131 | 1.148 | |
| noisePlot | 0.877 | 0.097 | 0.975 | |
| normalizeBins | 0.961 | 0.104 | 1.066 | |
| normalizeSegmentedBins | 6.156 | 0.256 | 6.415 | |
| plot | 1.440 | 0.142 | 1.583 | |
| poolRuns | 0.220 | 0.027 | 0.247 | |
| segmentBins | 5.979 | 0.181 | 6.162 | |
| smoothOutlierBins | 0.954 | 0.139 | 1.092 | |