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This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1595/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QDNAseq 1.36.0  (landing page)
Daoud Sie
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/QDNAseq
git_branch: RELEASE_3_17
git_last_commit: 22a474f
git_last_commit_date: 2023-04-25 10:30:57 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for QDNAseq on kjohnson2


To the developers/maintainers of the QDNAseq package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: QDNAseq
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:QDNAseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings QDNAseq_1.36.0.tar.gz
StartedAt: 2023-10-18 16:39:22 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 16:50:00 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 638.9 seconds
RetCode: 0
Status:   OK  
CheckDir: QDNAseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:QDNAseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings QDNAseq_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QDNAseq.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QDNAseq/DESCRIPTION’ ... OK
* this is package ‘QDNAseq’ version ‘1.36.0’
* 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
frequencyPlot          17.538  0.232  33.728
callBins               17.481  0.253  27.342
normalizeSegmentedBins  7.569  0.075  12.146
segmentBins             7.059  0.062  10.912
makeCgh                 2.162  0.045   5.082
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘QDNAseq,copyneutral.R’
  Running ‘QDNAseq,gain-copyneutral-gain.R’
  Running ‘QDNAseq,parallel-reproducibility.R’
  Running ‘QDNAseq.R’
  Running ‘binReadCounts.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: OK


Installation output

QDNAseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL QDNAseq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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)

Tests output

QDNAseq.Rcheck/tests/binReadCounts.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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)
> 
> if (requireNamespace("QDNAseq.hg19", quietly = TRUE)) {
+   bins <- getBinAnnotations(500, genome = "hg19")
+   print(bins)
+ 
+   bam <- system.file("extdata", "ex1.bam", package = "Rsamtools")
+   print(bam)
+ 
+   counts <- binReadCounts(bins, bamfiles = bam)
+   print(counts)
+ 
+   ## BUG: https://github.com/ccagc/QDNAseq/issues/89
+   counts2 <- binReadCounts(bins, bamfiles = bam, chunkSize = 10e3)
+   print(counts2)
+ }
Loaded bin annotations for genome 'hg19', bin size 500 kbp, and experiment type 'SR50' from annotation package QDNAseq.hg19 v1.30.0
QDNAseq bin annotations for Hsapiens, build hg19.
Created by Ilari Scheinin with QDNAseq 0.7.5, 2014-02-06 09:20:46.041402.
An object of class 'AnnotatedDataFrame'
  rowNames: 1:1-500000 1:500001-1000000 ... Y:59000001-59373566 (6206
    total)
  varLabels: chromosome start ... use (9 total)
  varMetadata: labelDescription
[1] "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rsamtools/extdata/ex1.bam"
    ex1 (1 of 1): extracting reads ... binning ...
QDNAseqReadCounts (storageMode: lockedEnvironment)
assayData: 6206 features, 1 samples 
  element names: counts 
protocolData: none
phenoData
  sampleNames: ex1
  varLabels: name total.reads used.reads expected.variance
  varMetadata: labelDescription
featureData
  featureNames: 1:1-500000 1:500001-1000000 ... Y:59000001-59373566
    (6206 total)
  fvarLabels: chromosome start ... use (9 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
    ex1 (1 of 1): extracting reads ...
binning chunk - seq1:1:10001
binning chunk - seq2:1:10001

QDNAseqReadCounts (storageMode: lockedEnvironment)
assayData: 6206 features, 1 samples 
  element names: counts 
protocolData: none
phenoData
  sampleNames: ex1
  varLabels: name total.reads used.reads expected.variance
  varMetadata: labelDescription
featureData
  featureNames: 1:1-500000 1:500001-1000000 ... Y:59000001-59373566
    (6206 total)
  fvarLabels: chromosome start ... use (9 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> 
> 
> 
> proc.time()
   user  system elapsed 
  7.251   0.338  11.738 

QDNAseq.Rcheck/tests/QDNAseq,copyneutral.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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)
> library(Biobase)
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> set.seed(0xBEEF)
> 
> 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:  
> 
> 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:  
> 
> dataC <- correctBins(dataF)
Calculating correction for GC content and mappability
    Calculating fit for sample LGG150 (1 of 1) ...
Done.
> 
> ## Force all copy neutral data
> cn <- assayDataElement(dataC, "copynumber")
> cn[,1] <- rnorm(nrow(cn), mean = 1.0, sd = 0.05)
> assayDataElement(dataC, "copynumber") <- cn
> 
> 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:  
> 
> 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:  
> 
> 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:  
> 
> fitC <- callBins(fit)
EM algorithm started ... 

[1] "Total number of segments present in the data: 4"
[1] "Number of segments used for fitting the model: 4"
39961468174332213.562.4770001014786712411.3112.9NA16384770001010146319411.377.5
Calling iteration1:

optim results
time: 0
minimum: 16682.0890247003
116682.0890247003-0.825303675797091-0.323169506423803-0.001754401929814960.2970863141060160.5078724084702190.9928769615298530.1100346090918040.0003692713871108020.0111811691191362-0.0001065348234756080.1102701734224670.145866377811007
39976518177753213.562.4770001014786712411.3112.9NA16384770001010146319411.377.5
Calling iteration2:

optim results
time: 0
minimum: 16682.0888522346
116682.0888522346-0.816384144994661-0.31848916294222-0.00167850977268490.292952991143050.5008064461942260.9819310567480430.1311557982956840.0002223141320088620.01118096583020170.0001872099918784220.1313921659017140.175722206269368
EM algorithm done ...

Computing posterior probabilities for all segments ...

Total time:0minutes

Adjusting segmented data for cellularity ... 

Cellularity sample1: 1

Adjusting normalized data for cellularity ... 

Cellularity sample1: 1

1
40003198399507213.764.1770001014786712411.3112.9NA16384770001010916422411.383.3
40003388566253213.765.4770001014786712411.3112.9NA16384770001010916422411.383.3
40003358566247213.765.4770001014786712411.3112.9NA16384770001010916422411.383.3
40003638833027213.767.4770001017824054411.3136NA16384770001010916422411.383.3
40007908833982213.767.4770001017824054411.3136NA16384770001010916422411.383.3
40007998833986213.767.4770001017824054411.3136NA16384770001010916422411.383.3
40008088833990213.767.4770001017824054411.3136NA16384770001010916422411.383.3
40008178833994213.767.4770001017824054411.3136NA16384770001010916422411.383.3
40008268833998213.767.4770001017824054411.3136NA16384770001010916422411.383.3
40008328834001213.767.4770001017824054411.3136NA16384770001010916422411.383.3
40008518900731213.768770001017824054411.3136NA16384770001010916422411.383.3
40012688901054213.768770001017824054411.3136NA16384770001010916422411.383.3
FINISHED!

Total time:0minutes

There were 24 warnings (use warnings() to see them)
> print(fitC)
QDNAseqCopyNumbers (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples 
  element names: calls, copynumber, probamp, probdloss, probgain, probloss, probnorm, 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:  
> 
> 
> ## Assert that everything is called copy-neutral
> calls <- assayDataElement(fitC, "calls")
> stopifnot(all(is.na(calls) | calls == 0))
> 
> formats <- c("tsv", "igv", "bed", "seg", "vcf")
> types <- c("copynumber", "segments", "calls")
> for (format in formats) {
+   for (type in types) {
+     fileext <- sprintf(".%s.%s", type, format)
+     file <- tempfile(pattern =  "QDNAseq-%s", fileext = fileext)
+     message(sprintf("  - exportBins(<%d samples>, format=\"%s\", type=\"%s\")", ncol(fitC), format, type))
+     file <- exportBins(fitC, format = format, type = type, file = file)
+     message(sprintf("    File(s) written: [n=%d] %s",
+             length(file), paste(sQuote(file), collapse = ", ")))
+     stopifnot(all(file_test("-f", file)))
+     if (format == "seg") {
+       segs <- read.table(file, sep = "\t", header = TRUE)
+       print(segs)
+       stopifnot(nrow(segs) == 0L)
+     } else if (format == "vcf") {
+       rows <- readLines(file)
+       rows <- grep("^#", rows, invert = TRUE, value = TRUE)
+       print(rows)
+       stopifnot(length(rows) == 0L)
+     }
+     file.remove(file)
+     stopifnot(!any(file_test("-f", file)))
+   }
+ }
  - exportBins(<1 samples>, format="tsv", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmphfMHbJ/QDNAseq-%seb1e40325647.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments")
    File(s) written: [n=1] '/tmp/RtmphfMHbJ/QDNAseq-%seb1e28be703e.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls")
    File(s) written: [n=1] '/tmp/RtmphfMHbJ/QDNAseq-%seb1e6ebb0b57.calls.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmphfMHbJ/QDNAseq-%seb1e39e5b58c.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments")
    File(s) written: [n=1] '/tmp/RtmphfMHbJ/QDNAseq-%seb1e17f21806.segments.igv'
  - exportBins(<1 samples>, format="igv", type="calls")
    File(s) written: [n=1] '/tmp/RtmphfMHbJ/QDNAseq-%seb1e17073e32.calls.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmphfMHbJ/QDNAseq-LGG150eb1e5c84506d.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments")
    File(s) written: [n=1] '/tmp/RtmphfMHbJ/QDNAseq-LGG150eb1e72bc538e.segments.bed'
  - exportBins(<1 samples>, format="bed", type="calls")
    File(s) written: [n=1] '/tmp/RtmphfMHbJ/QDNAseq-LGG150eb1e2a11ca7b.calls.bed'
  - exportBins(<1 samples>, format="seg", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmphfMHbJ/QDNAseq-LGG150eb1e760466d0.copynumber.seg'
[1] SAMPLE_NAME     CHROMOSOME      START           STOP           
[5] DATAPOINTS      LOG2_RATIO_MEAN
<0 rows> (or 0-length row.names)
  - exportBins(<1 samples>, format="seg", type="segments")
    File(s) written: [n=1] '/tmp/RtmphfMHbJ/QDNAseq-LGG150eb1e1afa1e38.segments.seg'
[1] SAMPLE_NAME     CHROMOSOME      START           STOP           
[5] DATAPOINTS      LOG2_RATIO_MEAN
<0 rows> (or 0-length row.names)
  - exportBins(<1 samples>, format="seg", type="calls")
    File(s) written: [n=1] '/tmp/RtmphfMHbJ/QDNAseq-LGG150eb1e1ad5fc5e.calls.seg'
[1] SAMPLE_NAME     CHROMOSOME      START           STOP           
[5] DATAPOINTS      LOG2_RATIO_MEAN
<0 rows> (or 0-length row.names)
  - exportBins(<1 samples>, format="vcf", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmphfMHbJ/QDNAseq-LGG150eb1e56ab8d15.copynumber.vcf'
character(0)
  - exportBins(<1 samples>, format="vcf", type="segments")
    File(s) written: [n=1] '/tmp/RtmphfMHbJ/QDNAseq-LGG150eb1e18bb8a27.segments.vcf'
character(0)
  - exportBins(<1 samples>, format="vcf", type="calls")
    File(s) written: [n=1] '/tmp/RtmphfMHbJ/QDNAseq-LGG150eb1e406b1320.calls.vcf'
character(0)
> 
> proc.time()
   user  system elapsed 
 19.174   0.657  30.346 

QDNAseq.Rcheck/tests/QDNAseq,gain-copyneutral-gain.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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)
> library(Biobase)
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(utils)
> set.seed(0xBEEF)
> 
> 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:  
> 
> 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:  
> 
> dataC <- correctBins(dataF)
Calculating correction for GC content and mappability
    Calculating fit for sample LGG150 (1 of 1) ...
Done.
> 
> ## Force results to have segments gain, copy neutral, and gain.
> cnAll <- assayDataElement(dataC, "copynumber")
> cnAll[,1] <- rnorm(nrow(cnAll), mean = 1.0, sd = 0.05)
> chr7 <- (chromosomes(dataC) == "7")
> cn <- cnAll[chr7, , drop = FALSE]
> n <- nrow(cn)
> idxs <- seq(from=1/3*n - 0.1*n, to=1/3*n + 0.1*n)
> cn[idxs,1] <- rnorm(length(idxs), mean = 2.0, sd = 0.05)
> idxs <- seq(from=2/3*n - 0.1*n, to=2/3*n + 0.1*n)
> cn[idxs,1] <- rnorm(length(idxs), mean = 2.0, sd = 0.05)
> cnAll[chr7, ] <- cn
> assayDataElement(dataC, "copynumber") <- cnAll
> 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:  
> 
> 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:  
> 
> 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:  
> 
> fitC <- callBins(fit)
EM algorithm started ... 

[1] "Total number of segments present in the data: 8"
[1] "Number of segments used for fitting the model: 8"
39964568217911213.562.7770001014786712411.3112.9NA16384770001010146319411.377.5
Calling iteration1:

optim results
time: 0
minimum: 16691.9360158015
116691.9360158015-0.76889026698241-0.310183146024425-0.01185150972096230.2885943760685340.4933553445096880.9879385470392230.0299884700901994-0.0005485736219481460.0111821966975442-4.08995447325668e-050.01000052582656670.0100005260086061
EM algorithm done ...

Computing posterior probabilities for all segments ...

Total time:0minutes

Adjusting segmented data for cellularity ... 

Cellularity sample1: 1

Adjusting normalized data for cellularity ... 

Cellularity sample1: 1

1
40006298442894213.764.5770001014786712411.3112.9NA16384770001010960127411.383.7
40006488609640213.765.7770001014786712411.3112.9NA16384770001010960127411.383.7
40006458609634213.765.7770001014786712411.3112.9NA16384770001010960127411.383.7
40006738878164213.767.8770001017824054411.3136NA16384770001010960127411.383.7
40011008879119213.767.8770001017824054411.3136NA16384770001010960127411.383.7
40011098879123213.767.8770001017824054411.3136NA16384770001010960127411.383.7
40011188879127213.767.8770001017824054411.3136NA16384770001010960127411.383.7
40011278879131213.767.8770001017824054411.3136NA16384770001010960127411.383.7
40011368879135213.767.8770001017824054411.3136NA16384770001010960127411.383.7
40011428879138213.767.8770001017824054411.3136NA16384770001010960127411.383.7
40011618945868213.768.3770001017824054411.3136NA16384770001010960127411.383.7
40015788946191213.868.3770001017824054411.3136NA16384770001010960127411.383.7
FINISHED!

Total time:0minutes

There were 32 warnings (use warnings() to see them)
> print(fitC)
QDNAseqCopyNumbers (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples 
  element names: calls, copynumber, probamp, probdloss, probgain, probloss, probnorm, 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:  
> 
> ## Assert that everything is called copy-neutral
> calls <- assayDataElement(fitC, "calls")
> stopifnot(all(is.na(calls) | calls %in% c(0, 2)))
> 
> formats <- c("tsv", "igv", "bed", "seg", "vcf")
> types <- c("copynumber", "segments", "calls")
> for (format in formats) {
+   for (type in types) {
+     fileext <- sprintf(".%s.%s", type, format)
+     file <- tempfile(pattern =  "QDNAseq-%s", fileext = fileext)
+     message(sprintf("  - exportBins(<%d samples>, format=\"%s\", type=\"%s\")", ncol(fitC), format, type))
+     file <- exportBins(fitC, format = format, type = type, file = file)
+     message(sprintf("    File(s) written: [n=%d] %s",
+             length(file), paste(sQuote(file), collapse = ", ")))
+     stopifnot(all(file_test("-f", file)))
+ 
+     if (format == "seg") {
+       segs <- read.table(file, sep = "\t", header = TRUE)
+       print(segs)
+       stopifnot(all(segs$CHROMOSOME == "7"), nrow(segs) == 2L)
+     } else if (format == "vcf") {
+       segs <- read.table(file, sep = "\t", header = FALSE)
+       print(segs)
+       stopifnot(all(segs$V1 == "7"), nrow(segs) == 2L)
+     }
+ 
+     file.remove(file)
+     stopifnot(!any(file_test("-f", file)))
+   }
+ }
  - exportBins(<1 samples>, format="tsv", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmpUirG7S/QDNAseq-%seb6d22588dc0.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments")
    File(s) written: [n=1] '/tmp/RtmpUirG7S/QDNAseq-%seb6d63c249dd.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls")
    File(s) written: [n=1] '/tmp/RtmpUirG7S/QDNAseq-%seb6d687f7f55.calls.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmpUirG7S/QDNAseq-%seb6da80db0c.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments")
    File(s) written: [n=1] '/tmp/RtmpUirG7S/QDNAseq-%seb6d11acf637.segments.igv'
  - exportBins(<1 samples>, format="igv", type="calls")
    File(s) written: [n=1] '/tmp/RtmpUirG7S/QDNAseq-%seb6d72589df1.calls.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmpUirG7S/QDNAseq-LGG150eb6d17e973dd.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments")
    File(s) written: [n=1] '/tmp/RtmpUirG7S/QDNAseq-LGG150eb6d5fb5be6e.segments.bed'
  - exportBins(<1 samples>, format="bed", type="calls")
    File(s) written: [n=1] '/tmp/RtmpUirG7S/QDNAseq-LGG150eb6d14e958d9.calls.bed'
  - exportBins(<1 samples>, format="seg", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmpUirG7S/QDNAseq-LGG150eb6d63c81948.copynumber.seg'
                                                SAMPLE_NAME CHROMOSOME    START
1 /tmp/RtmpUirG7S/QDNAseq-LGG150eb6d63c81948.copynumber.seg          7 37110001
2 /tmp/RtmpUirG7S/QDNAseq-LGG150eb6d63c81948.copynumber.seg          7 90165001
       STOP DATAPOINTS LOG2_RATIO_MEAN
1  68955000       1487            0.99
2 122010000       2012            0.99
  - exportBins(<1 samples>, format="seg", type="segments")
    File(s) written: [n=1] '/tmp/RtmpUirG7S/QDNAseq-LGG150eb6d65f3f925.segments.seg'
                                              SAMPLE_NAME CHROMOSOME    START
1 /tmp/RtmpUirG7S/QDNAseq-LGG150eb6d65f3f925.segments.seg          7 37110001
2 /tmp/RtmpUirG7S/QDNAseq-LGG150eb6d65f3f925.segments.seg          7 90165001
       STOP DATAPOINTS LOG2_RATIO_MEAN
1  68955000       1487            0.99
2 122010000       2012            0.99
  - exportBins(<1 samples>, format="seg", type="calls")
    File(s) written: [n=1] '/tmp/RtmpUirG7S/QDNAseq-LGG150eb6d746a206d.calls.seg'
                                           SAMPLE_NAME CHROMOSOME    START
1 /tmp/RtmpUirG7S/QDNAseq-LGG150eb6d746a206d.calls.seg          7 37110001
2 /tmp/RtmpUirG7S/QDNAseq-LGG150eb6d746a206d.calls.seg          7 90165001
       STOP DATAPOINTS LOG2_RATIO_MEAN
1  68955000       1487            0.99
2 122010000       2012            0.99
  - exportBins(<1 samples>, format="vcf", type="copynumber")
    File(s) written: [n=1] '/tmp/RtmpUirG7S/QDNAseq-LGG150eb6d63770fd0.copynumber.vcf'
  V1       V2 V3    V4    V5   V6   V7
1  7 37110001  . <DIP> <DUP> 1000 PASS
2  7 90165001  . <DIP> <DUP> 1000 PASS
                                                                      V8 V9 V10
1  SVTYPE=DUP;END=68955000;SVLEN=31845000;BINS=1487;SCORE=2;LOG2CNT=0.99 GT 0/1
2 SVTYPE=DUP;END=122010000;SVLEN=31845000;BINS=2012;SCORE=2;LOG2CNT=0.99 GT 0/1
  - exportBins(<1 samples>, format="vcf", type="segments")
    File(s) written: [n=1] '/tmp/RtmpUirG7S/QDNAseq-LGG150eb6d1daf53b4.segments.vcf'
  V1       V2 V3    V4    V5   V6   V7
1  7 37110001  . <DIP> <DUP> 1000 PASS
2  7 90165001  . <DIP> <DUP> 1000 PASS
                                                                      V8 V9 V10
1  SVTYPE=DUP;END=68955000;SVLEN=31845000;BINS=1487;SCORE=2;LOG2CNT=0.99 GT 0/1
2 SVTYPE=DUP;END=122010000;SVLEN=31845000;BINS=2012;SCORE=2;LOG2CNT=0.99 GT 0/1
  - exportBins(<1 samples>, format="vcf", type="calls")
    File(s) written: [n=1] '/tmp/RtmpUirG7S/QDNAseq-LGG150eb6d61a05da5.calls.vcf'
  V1       V2 V3    V4    V5   V6   V7
1  7 37110001  . <DIP> <DUP> 1000 PASS
2  7 90165001  . <DIP> <DUP> 1000 PASS
                                                                      V8 V9 V10
1  SVTYPE=DUP;END=68955000;SVLEN=31845000;BINS=1487;SCORE=2;LOG2CNT=0.99 GT 0/1
2 SVTYPE=DUP;END=122010000;SVLEN=31845000;BINS=2012;SCORE=2;LOG2CNT=0.99 GT 0/1
> 
> proc.time()
   user  system elapsed 
 19.085   0.645  30.557 

QDNAseq.Rcheck/tests/QDNAseq,parallel-reproducibility.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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")
> 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
> set.seed(42)  ## segmentBins() relies on RNG via DNAcopy::segment()
> 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", "multisession")
> if (parallelly::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))
+   
+   set.seed(42)  ## segmentBins() relies on RNG via DNAcopy::segment()
+   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("multisession") ...
    Calculating fit for sample LGG150 (1 of 1) ...
    Segmenting: LGG150 (1 of 1) ...
Reproducibility with plan("multisession") ... done
Reproducibility with plan("multicore") ...
Reproducibility with plan("multicore") ... done
There were 50 or more warnings (use warnings() to see the first 50)
> 
> future::plan(oplan)
> 
> proc.time()
   user  system elapsed 
 63.959   1.412 113.440 

QDNAseq.Rcheck/tests/QDNAseq.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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)
> library(Biobase) ## combine(), sampleNames()
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(utils)
> 
> # 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)
EM algorithm started ... 

[1] "Total number of segments present in the data: 10"
[1] "Number of segments used for fitting the model: 9"
40103878180843214.262.5770001014818882411.3113.1NA16384770001012282402411.393.8
Calling iteration1:

optim results
time: 1
minimum: 16445.6418287481
116443.1634295677-0.939948404909664-0.5351158716347120.04999922851584940.1357341814220170.2320391157632851.492692224927890.46336036623653-0.0007447487965542740.0111894143724591-0.000962583906213420.3145629342085070.798554843389167
40118928184294214.362.5770001014818882411.3113.1NA16384770001012282402411.393.8
Calling iteration2:

optim results
time: 0
minimum: 16445.5781374328
116443.1331012469-0.932876677515083-0.535943303880990.0499979048415910.1114729434735370.1905642555481931.861013902305770.4314700360573740.000144068768407330.01118427659401560.0007568920162792620.2061088124299370.87402235157801
40118928184294214.362.5770001014818882411.3113.1NA16384770001012282402411.393.8
Calling iteration3:

optim results
time: 0
minimum: 16445.5975371627
116443.1273697069-0.924012853099601-0.5365177469718870.04999923288882760.108573194240180.1856071014916831.753751992204390.4694950401327692.9331320413768e-050.0111878614439676-0.0001759851682342870.07360543573369820.943675664015282
EM algorithm done ...

Computing posterior probabilities for all segments ...

Total time:0minutes

Adjusting segmented data for cellularity ... 

Cellularity sample1: 1

Adjusting normalized data for cellularity ... 

Cellularity sample1: 1

1
40145608405528214.564.2770001014818882411.3113.1NA16384770001012282402411.393.8
40145798572274214.565.5770001014818882411.3113.1NA16384770001012282402411.393.8
40145768572268214.565.5770001014818882411.3113.1NA16384770001012282402411.393.8
40146048839283214.567.5770001017862658411.3136.3NA16384770001012282402411.393.8
40150318840238214.567.5770001017862658411.3136.3NA16384770001012282402411.393.8
40150408840242214.567.5770001017862658411.3136.3NA16384770001012282402411.393.8
40150498840246214.567.5770001017862658411.3136.3NA16384770001012282402411.393.8
40150588840250214.567.5770001017862658411.3136.3NA16384770001012282402411.393.8
40150678840254214.567.5770001017862658411.3136.3NA16384770001012282402411.393.8
40150738840257214.567.5770001017862658411.3136.3NA16384770001012282402411.393.8
40150928906987214.568770001017862658411.3136.3NA16384770001012282402411.393.8
40155098907310214.568770001017862658411.3136.3NA16384770001012282402411.393.8
FINISHED!

Total time:0minutes

There were 50 or more warnings (use warnings() to see the first 50)
> print(fitC)
QDNAseqCopyNumbers (storageMode: lockedEnvironment)
assayData: 38819 features, 1 samples 
  element names: calls, copynumber, probamp, probdloss, probgain, probloss, probnorm, 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(fitC)
Plotting sample LGG150 (1 of 1) ...
> 
> 
> # ---------------------------------------------------------------
> # Exporting
> # ---------------------------------------------------------------
> message("* exportBins() ...")
* exportBins() ...
> 
> sets <- list(data = data, dataC = dataC, fit = fit, fitC = fitC)
> for (name in names(sets)) {
+   set <- sets[[name]]
+   formats <- c("tsv", "igv", "bed")
+   if (name == "fitC") formats <- c(formats, "vcf", "seg")
+   for (format in formats) {
+     types <- c("copynumber")
+     if (name %in% c("fit", "fitC")) types <- c(types, "segments")
+     if (name == "fitC") types <- c(types, "calls")
+     for (type in types) {
+       fileext <- sprintf(".%s.%s", type, format)
+       templates <- c("QDNAseq-%s.", "QDNAseq-%i.", "QDNAseq-%03i.")
+       if (ncol(set) == 1L || !(format %in% c("bed", "seg", "vcf"))) {
+         templates <- c("QDNAseq.", templates)
+       }
+       for (template in templates) {
+         file <- tempfile(pattern = template, fileext = fileext)
+         message(sprintf("  - exportBins(<%d samples>, format=\"%s\", type=\"%s\", file=\"%s\")", ncol(set), format, type, template))
+         file <- exportBins(set, file = file, format = format, type = type)
+         message(sprintf("    File(s) written: [n=%d] %s",
+                 length(file), paste(sQuote(file), collapse = ", ")))
+         stopifnot(all(file_test("-f", file)))
+         file.remove(file)
+         stopifnot(!any(file_test("-f", file)))
+       }
+     }
+   }
+ }
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f01754685dad.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f017fde3426.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0174531b2ed.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f01741da0918.copynumber.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f017518b286e.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f01770b7795.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0171d7dad0.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f01725e8ea2.copynumber.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f017de62ee5.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-LGG150.f017310c384.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-1.f017419410ae.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-001.f0175fd33124.copynumber.bed'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f017223f63a2.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f0176fa6323e.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f01782cbdb6.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f017315afbeb.copynumber.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0174c511a9d.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f01760aa608f.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f01751a97ddd.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f0174e86620d.copynumber.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f017588f6bc1.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-LGG150.f0172feb7953.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-1.f017c6a50b9.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-001.f01717d9a80d.copynumber.bed'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f01752a7f9b6.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f01711fb461f.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0177b8a672.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f0176bb78a53.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0175eda8664.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f0175cad3fe2.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f017723d3df6.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f01712af1c12.segments.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f017265beb53.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f0175cb6a9d1.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0175c4707e4.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f0173b573910.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0175b6367df.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f0175b389058.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0175e8cb031.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f01766839175.segments.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f01747c2cce7.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-LGG150.f017461a767f.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-1.f0177359afcd.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-001.f017524f6e5.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0173dcd3706.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-LGG150.f0176bd78a9c.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-1.f01713cd3f14.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-001.f0177e84434.segments.bed'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f01721d5b5fa.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f017559e4170.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0178da4bfa.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f01733b20ea0.copynumber.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0176ede44e3.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f017427ccbf2.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f017f319ef8.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f0172bbb393.segments.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f017710a794b.calls.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f01766a164e7.calls.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0176de7ae54.calls.tsv'
  - exportBins(<1 samples>, format="tsv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f017566452b.calls.tsv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0177d470cd1.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f017439aad98.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0175ffaf8d4.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f01755e65786.copynumber.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f01757c4a79.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f01722fd50bf.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f01724c03d8b.segments.igv'
  - exportBins(<1 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f01749088386.segments.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0174df2f7df.calls.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f017a6f7974.calls.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0171c8eb406.calls.igv'
  - exportBins(<1 samples>, format="igv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f0175ccd048f.calls.igv'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f01717e677e2.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-LGG150.f0171bc8a2b0.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-1.f0171130df10.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-001.f0171f849c41.copynumber.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0173b2e7f91.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-LGG150.f01769b926f1.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-1.f0177aabce70.segments.bed'
  - exportBins(<1 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-001.f017257e59fb.segments.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f017a4580f8.calls.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-LGG150.f01759161f0c.calls.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-1.f0173b507a85.calls.bed'
  - exportBins(<1 samples>, format="bed", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-001.f017209bd02f.calls.bed'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0175580ce62.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-LGG150.f0177b6dafc8.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-1.f0175e2fb2c6.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-001.f017d821579.copynumber.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f017574fc1dc.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-LGG150.f01735407f4c.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-1.f0171d6571e4.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-001.f0176f183ecf.segments.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f01720c3c104.calls.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-LGG150.f01713b4fe6a.calls.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-1.f0174faaeb41.calls.vcf'
  - exportBins(<1 samples>, format="vcf", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-001.f0175e3b2143.calls.vcf'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0177c04e609.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-LGG150.f017259a987b.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-1.f0174890c686.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-001.f01718d9aca2.copynumber.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0177ad4cc6c.segments.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-LGG150.f01728b90574.segments.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-1.f017b15178f.segments.seg'
  - exportBins(<1 samples>, format="seg", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-001.f01715bdb2f8.segments.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0175930c2ee.calls.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-LGG150.f017104dc501.calls.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-1.f01761c0cd03.calls.seg'
  - exportBins(<1 samples>, format="seg", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-001.f01738d3b218.calls.seg'
> 
> sets <- list(data = data, dataC = dataC, fit = fit, fitC = fitC)
> sets <- lapply(sets, FUN = function(set) {
+   stopifnot(ncol(set) == 1L)
+   name <- sampleNames(set)
+   setA <- set
+   sampleNames(setA) <- sprintf("%sa", name)
+   setB <- set
+   sampleNames(setB) <- sprintf("%sb", name)
+   combine(setA, setB)
+ })
> 
> for (name in names(sets)) {
+   set <- sets[[name]]
+   stopifnot(ncol(set) == 2L)
+   formats <- c("tsv", "igv", "bed")
+   if (name == "fitC") formats <- c(formats, "vcf", "seg")
+   for (format in formats) {
+     types <- c("copynumber")
+     if (name %in% c("fit", "fitC")) types <- c(types, "segments")
+     if (name == "fitC") types <- c(types, "calls")
+     for (type in types) {
+       fileext <- sprintf(".%s.%s", type, format)
+       templates <- c("QDNAseq-%s.", "QDNAseq-%i.", "QDNAseq-%03i.")
+       if (ncol(set) == 1L || !(format %in% c("bed", "seg", "vcf"))) {
+         templates <- c("QDNAseq.", templates)
+       }
+       for (template in templates) {
+         file <- tempfile(pattern = template, fileext = fileext)
+         message(sprintf("  - exportBins(<%d samples>, format=\"%s\", type=\"%s\", file=\"%s\")", ncol(set), format, type, template))
+         file <- exportBins(set, file = file, format = format, type = type)
+         message(sprintf("    File(s) written: [n=%d] %s",
+                 length(file), paste(sQuote(file), collapse = ", ")))
+         stopifnot(all(file_test("-f", file)))
+         file.remove(file)
+         stopifnot(!any(file_test("-f", file)))
+       }
+     }
+   }
+ }
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f017525162cd.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f0175d2daaf3.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0176132674f.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f017341ca563.copynumber.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f01744ae214f.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f01740cecc3.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0176c8bf848.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f017595976a4.copynumber.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-LGG150a.f0177c36d0.copynumber.bed', '/tmp/RtmprJ9iu9/QDNAseq-LGG150b.f0177c36d0.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-1.f0175af291ef.copynumber.bed', '/tmp/RtmprJ9iu9/QDNAseq-2.f0175af291ef.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-001.f0176b4b108e.copynumber.bed', '/tmp/RtmprJ9iu9/QDNAseq-002.f0176b4b108e.copynumber.bed'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f017d2c11aa.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f017483bb6a7.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0174854b2fd.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f01730b32524.copynumber.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f017414b7776.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f01741900577.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0175656e941.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f01763ebd6af.copynumber.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-LGG150a.f017105bae69.copynumber.bed', '/tmp/RtmprJ9iu9/QDNAseq-LGG150b.f017105bae69.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-1.f017731777e2.copynumber.bed', '/tmp/RtmprJ9iu9/QDNAseq-2.f017731777e2.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-001.f0179bfd176.copynumber.bed', '/tmp/RtmprJ9iu9/QDNAseq-002.f0179bfd176.copynumber.bed'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f01710509efa.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f0171cf53774.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f017270baf86.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f01770309a70.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0176eb689b.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f01749209ba9.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0177bcb99c0.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f01773db4bbe.segments.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0174249e25e.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f017acab52.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f017482394d6.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f0171800929a.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0174d98c8c5.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f01769a5254f.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f01759349bb8.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f017cdb7ac9.segments.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-LGG150a.f0171d5a28b7.copynumber.bed', '/tmp/RtmprJ9iu9/QDNAseq-LGG150b.f0171d5a28b7.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-1.f017a27156f.copynumber.bed', '/tmp/RtmprJ9iu9/QDNAseq-2.f017a27156f.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-001.f017bf02f9e.copynumber.bed', '/tmp/RtmprJ9iu9/QDNAseq-002.f017bf02f9e.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-LGG150a.f01745c63431.segments.bed', '/tmp/RtmprJ9iu9/QDNAseq-LGG150b.f01745c63431.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-1.f017578ca0c0.segments.bed', '/tmp/RtmprJ9iu9/QDNAseq-2.f017578ca0c0.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-001.f017518dca27.segments.bed', '/tmp/RtmprJ9iu9/QDNAseq-002.f017518dca27.segments.bed'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f01733d2f045.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f0175d9c5c97.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0174482ed84.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f0176fb7983f.copynumber.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0177e6c8965.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f0177b086bb.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f017565d62ee.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f017d0a238e.segments.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f01714a44652.calls.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f0172d04bc14.calls.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f01711d7dc23.calls.tsv'
  - exportBins(<2 samples>, format="tsv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f01772b586fb.calls.tsv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f0176bb10392.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f01732619d7a.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f01726a9ce6d.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f017562f69ef.copynumber.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f01742d3f61d.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f01769c30c31.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f0174559b36.segments.igv'
  - exportBins(<2 samples>, format="igv", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f0171040f873.segments.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq.f01719774e5b.calls.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%s.f01767b9456c.calls.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%i.f017347ceaa7.calls.igv'
  - exportBins(<2 samples>, format="igv", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=1] '/tmp/RtmprJ9iu9/QDNAseq-%03i.f017751194dc.calls.igv'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-LGG150a.f0175544338f.copynumber.bed', '/tmp/RtmprJ9iu9/QDNAseq-LGG150b.f0175544338f.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-1.f01770951d04.copynumber.bed', '/tmp/RtmprJ9iu9/QDNAseq-2.f01770951d04.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-001.f0174da42b5a.copynumber.bed', '/tmp/RtmprJ9iu9/QDNAseq-002.f0174da42b5a.copynumber.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-LGG150a.f017551a4988.segments.bed', '/tmp/RtmprJ9iu9/QDNAseq-LGG150b.f017551a4988.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-1.f01730d1ab5e.segments.bed', '/tmp/RtmprJ9iu9/QDNAseq-2.f01730d1ab5e.segments.bed'
  - exportBins(<2 samples>, format="bed", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-001.f0171549c15c.segments.bed', '/tmp/RtmprJ9iu9/QDNAseq-002.f0171549c15c.segments.bed'
  - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-LGG150a.f0171d3589ef.calls.bed', '/tmp/RtmprJ9iu9/QDNAseq-LGG150b.f0171d3589ef.calls.bed'
  - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-1.f01725f2b8e4.calls.bed', '/tmp/RtmprJ9iu9/QDNAseq-2.f01725f2b8e4.calls.bed'
  - exportBins(<2 samples>, format="bed", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-001.f01762489432.calls.bed', '/tmp/RtmprJ9iu9/QDNAseq-002.f01762489432.calls.bed'
  - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-LGG150a.f017af99107.copynumber.vcf', '/tmp/RtmprJ9iu9/QDNAseq-LGG150b.f017af99107.copynumber.vcf'
  - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-1.f0176a06832.copynumber.vcf', '/tmp/RtmprJ9iu9/QDNAseq-2.f0176a06832.copynumber.vcf'
  - exportBins(<2 samples>, format="vcf", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-001.f017d18ae04.copynumber.vcf', '/tmp/RtmprJ9iu9/QDNAseq-002.f017d18ae04.copynumber.vcf'
  - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-LGG150a.f0174f488f53.segments.vcf', '/tmp/RtmprJ9iu9/QDNAseq-LGG150b.f0174f488f53.segments.vcf'
  - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-1.f01724b9bacf.segments.vcf', '/tmp/RtmprJ9iu9/QDNAseq-2.f01724b9bacf.segments.vcf'
  - exportBins(<2 samples>, format="vcf", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-001.f0171d977edf.segments.vcf', '/tmp/RtmprJ9iu9/QDNAseq-002.f0171d977edf.segments.vcf'
  - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-LGG150a.f017450a71a6.calls.vcf', '/tmp/RtmprJ9iu9/QDNAseq-LGG150b.f017450a71a6.calls.vcf'
  - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-1.f01730ab6cb3.calls.vcf', '/tmp/RtmprJ9iu9/QDNAseq-2.f01730ab6cb3.calls.vcf'
  - exportBins(<2 samples>, format="vcf", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-001.f017466d74bb.calls.vcf', '/tmp/RtmprJ9iu9/QDNAseq-002.f017466d74bb.calls.vcf'
  - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-LGG150a.f0173c0ac51c.copynumber.seg', '/tmp/RtmprJ9iu9/QDNAseq-LGG150b.f0173c0ac51c.copynumber.seg'
  - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-1.f0176712d00f.copynumber.seg', '/tmp/RtmprJ9iu9/QDNAseq-2.f0176712d00f.copynumber.seg'
  - exportBins(<2 samples>, format="seg", type="copynumber", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-001.f017419bda7.copynumber.seg', '/tmp/RtmprJ9iu9/QDNAseq-002.f017419bda7.copynumber.seg'
  - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-LGG150a.f01735f2210b.segments.seg', '/tmp/RtmprJ9iu9/QDNAseq-LGG150b.f01735f2210b.segments.seg'
  - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-1.f0172b5774d8.segments.seg', '/tmp/RtmprJ9iu9/QDNAseq-2.f0172b5774d8.segments.seg'
  - exportBins(<2 samples>, format="seg", type="segments", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-001.f0177ab82722.segments.seg', '/tmp/RtmprJ9iu9/QDNAseq-002.f0177ab82722.segments.seg'
  - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%s.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-LGG150a.f0175011681f.calls.seg', '/tmp/RtmprJ9iu9/QDNAseq-LGG150b.f0175011681f.calls.seg'
  - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-1.f01726caf44a.calls.seg', '/tmp/RtmprJ9iu9/QDNAseq-2.f01726caf44a.calls.seg'
  - exportBins(<2 samples>, format="seg", type="calls", file="QDNAseq-%03i.")
    File(s) written: [n=2] '/tmp/RtmprJ9iu9/QDNAseq-001.f017566c3a2b.calls.seg', '/tmp/RtmprJ9iu9/QDNAseq-002.f017566c3a2b.calls.seg'
> 
> message("* exportBins() ... done")
* exportBins() ... done
> 
> proc.time()
   user  system elapsed 
 68.215   4.339 109.927 

Example timings

QDNAseq.Rcheck/QDNAseq-Ex.timings

nameusersystemelapsed
addPhenodata0.1300.0070.207
applyFilters0.630.010.98
binReadCounts0.0000.0000.001
callBins17.481 0.25327.342
compareToReference2.2080.0403.468
correctBins2.0030.0253.120
createBins0.0000.0000.001
estimateCorrection1.9660.0243.102
exportBins0.0000.0000.001
frequencyPlot17.538 0.23233.728
getBinAnnotations000
highlightFilters0.5890.0651.545
isobarPlot1.2770.0273.067
makeCgh2.1620.0455.082
noisePlot1.9930.0274.770
normalizeBins2.0220.0264.246
normalizeSegmentedBins 7.569 0.07512.146
plot2.5040.0803.957
poolRuns0.1430.0050.227
segmentBins 7.059 0.06210.912
smoothOutlierBins2.1400.0433.374