Daoud Sie
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/QDNAseq |
| Branch: RELEASE_3_12 |
| Last Commit: 312b6c8 |
| Last Changed Date: 2020-10-27 10:55:28 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:57 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the QDNAseq package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1423/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| QDNAseq 1.26.0 (landing page) Daoud Sie
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: QDNAseq |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QDNAseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings QDNAseq_1.26.0.tar.gz |
| StartedAt: 2021-05-06 05:52:18 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:02:18 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 600.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: QDNAseq.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QDNAseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings QDNAseq_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/QDNAseq.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.26.0'
* 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-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/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-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/QDNAseq/man/binReadCounts.Rd:29: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/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-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/QDNAseq/man/getBinAnnotations.Rd:48: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/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-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/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-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/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-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/QDNAseq/man/makeCgh.Rd:39: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/QDNAseq/man/noisePlot.Rd:28: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-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 ... NOTE
Namespace in Imports field not imported from: 'future'
All declared Imports should be used.
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
callBins 25.41 0.28 25.70
frequencyPlot 24.87 0.05 24.92
segmentBins 15.44 0.00 15.44
normalizeSegmentedBins 15.10 0.01 15.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
frequencyPlot 25.95 0.01 25.97
callBins 24.17 0.22 24.41
normalizeSegmentedBins 9.91 0.01 9.93
segmentBins 8.11 0.02 8.12
* 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: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/QDNAseq.Rcheck/00check.log'
for details.
QDNAseq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/QDNAseq_1.26.0.tar.gz && rm -rf QDNAseq.buildbin-libdir && mkdir QDNAseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=QDNAseq.buildbin-libdir QDNAseq_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL QDNAseq_1.26.0.zip && rm QDNAseq_1.26.0.tar.gz QDNAseq_1.26.0.zip
###
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% 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 580k 100 580k 0 0 5316k 0 --:--:-- --:--:-- --:--:-- 5372k
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-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/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-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/QDNAseq/man/binReadCounts.Rd:29: 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-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/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-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/QDNAseq/man/getBinAnnotations.Rd:48: 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-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/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-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/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-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/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-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/QDNAseq/man/makeCgh.Rd:39: file link 'cghCall' in package 'CGHbase' does not exist and so has been treated as a topic
noisePlot html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp6fHl92/R.INSTALL1aac6a032cd7/QDNAseq/man/noisePlot.Rd:28: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
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_1.26.0.zip
* DONE (QDNAseq)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'QDNAseq' successfully unpacked and MD5 sums checked
|
QDNAseq.Rcheck/tests_i386/QDNAseq.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
26.87 0.59 27.43
|
QDNAseq.Rcheck/tests_x64/QDNAseq.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
19.57 0.42 19.98
|
|
QDNAseq.Rcheck/tests_i386/QDNAseq,reproducibility.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
> options("QDNAseq::verbose"=FALSE)
>
> # Load data
> data(LGG150)
> data <- LGG150
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # TRUTH
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Filter out "bad" bins
> dataF <- applyFilters(data, residual=TRUE, blacklist=TRUE)
>
> # Correct read counts as a function of GC content and mappability
> dataC <- correctBins(dataF)
>
> # Normalize binned read counts to have diploid normal copy number
> dataN <- normalizeBins(dataC)
>
> # Segment copy numbers
> fit <- segmentBins(dataN)
>
> # Call copy-number segments
> fitC <- callBins(fit)
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # REPRODUCIBILITY
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> strategies <- c("sequential", "multiprocess")
> if (future::supportsMulticore()) strategies <- c(strategies, "multicore")
>
> oplan <- future::plan("list")
> for (strategy in strategies) {
+ message(sprintf("Reproducibility with plan(\"%s\") ...", strategy))
+
+ future::plan(strategy)
+
+ dataFr <- applyFilters(data, residual=TRUE, blacklist=TRUE)
+ stopifnot(all.equal(dataFr, dataF))
+
+ dataCr <- correctBins(dataF)
+ stopifnot(all.equal(dataCr, dataC))
+
+ dataNr <- normalizeBins(dataC)
+ stopifnot(all.equal(dataNr, dataN))
+
+ fitr <- segmentBins(dataNr)
+ stopifnot(all.equal(fitr, fit))
+
+ fitCr <- callBins(fitr)
+ stopifnot(all.equal(fitCr, fitC))
+
+ message(sprintf("Reproducibility with plan(\"%s\") ... done", strategy))
+ }
Reproducibility with plan("sequential") ...
Reproducibility with plan("sequential") ... done
Reproducibility with plan("multiprocess") ...
Calculating fit for sample LGG150 (1 of 1) ...
Segmenting: LGG150 (1 of 1) ...
Reproducibility with plan("multiprocess") ... done
There were 50 or more warnings (use warnings() to see the first 50)
>
> future::plan(oplan)
>
> proc.time()
user system elapsed
65.23 0.87 84.62
|
QDNAseq.Rcheck/tests_x64/QDNAseq,reproducibility.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.
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Type 'q()' to quit R.
> ######################################################################
> # This scripts asserts that for each processing step of QDNAseq
> # the output/results are reproducible (numerically equal).
> ######################################################################
> library("QDNAseq")
> options("QDNAseq::verbose"=FALSE)
>
> # Load data
> data(LGG150)
> data <- LGG150
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # TRUTH
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Filter out "bad" bins
> dataF <- applyFilters(data, residual=TRUE, blacklist=TRUE)
>
> # Correct read counts as a function of GC content and mappability
> dataC <- correctBins(dataF)
>
> # Normalize binned read counts to have diploid normal copy number
> dataN <- normalizeBins(dataC)
>
> # Segment copy numbers
> fit <- segmentBins(dataN)
>
> # Call copy-number segments
> fitC <- callBins(fit)
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # REPRODUCIBILITY
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> strategies <- c("sequential", "multiprocess")
> if (future::supportsMulticore()) strategies <- c(strategies, "multicore")
>
> oplan <- future::plan("list")
> for (strategy in strategies) {
+ message(sprintf("Reproducibility with plan(\"%s\") ...", strategy))
+
+ future::plan(strategy)
+
+ dataFr <- applyFilters(data, residual=TRUE, blacklist=TRUE)
+ stopifnot(all.equal(dataFr, dataF))
+
+ dataCr <- correctBins(dataF)
+ stopifnot(all.equal(dataCr, dataC))
+
+ dataNr <- normalizeBins(dataC)
+ stopifnot(all.equal(dataNr, dataN))
+
+ fitr <- segmentBins(dataNr)
+ stopifnot(all.equal(fitr, fit))
+
+ fitCr <- callBins(fitr)
+ stopifnot(all.equal(fitCr, fitC))
+
+ message(sprintf("Reproducibility with plan(\"%s\") ... done", strategy))
+ }
Reproducibility with plan("sequential") ...
Reproducibility with plan("sequential") ... done
Reproducibility with plan("multiprocess") ...
Calculating fit for sample LGG150 (1 of 1) ...
Segmenting: LGG150 (1 of 1) ...
Reproducibility with plan("multiprocess") ... done
There were 50 or more warnings (use warnings() to see the first 50)
>
> future::plan(oplan)
>
> proc.time()
user system elapsed
61.59 0.78 79.17
|
|
QDNAseq.Rcheck/examples_i386/QDNAseq-Ex.timings
|
QDNAseq.Rcheck/examples_x64/QDNAseq-Ex.timings
|