Gavin Ha
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/TitanCNA |
| Branch: RELEASE_3_6 |
| Last Commit: 21742ca |
| Last Changed Date: 2017-10-30 12:40:14 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:38:32 -0400 (Thu, 12 Apr 2018).
| Package 1402/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TitanCNA 1.16.0 Gavin Ha
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| Package: TitanCNA |
| Version: 1.16.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TitanCNA_1.16.0.tar.gz |
| StartedAt: 2018-04-12 10:20:42 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 10:26:10 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 327.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TitanCNA.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TitanCNA_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/TitanCNA.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TitanCNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TitanCNA’ version ‘1.16.0’
* 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 ‘TitanCNA’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::slice’ by ‘dplyr::slice’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomeInfoDb::intersect’ by ‘dplyr::intersect’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::desc’ by ‘dplyr::desc’ when loading ‘TitanCNA’
Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’
See ‘/Users/biocbuild/bbs-3.6-bioc/meat/TitanCNA.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 7.5Mb
sub-directories of 1Mb or more:
data 1.7Mb
extdata 4.9Mb
* 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 loading without being on the library search path ... 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 ... NOTE
computeSDbwIndex: no visible binding for global variable ‘CopyNumber’
computeSDbwIndex: no visible binding for global variable
‘ClonalCluster’
computeSDbwIndex: no visible binding for global variable ‘TITANstate’
computeSDbwIndex: no visible binding for global variable ‘TITANcall’
correctIntegerCN: no visible binding for global variable ‘Chromosome’
correctIntegerCN: no visible binding for global variable ‘Copy_Number’
correctIntegerCN: no visible binding for global variable
‘logR_Copy_Number’
correctIntegerCN: no visible binding for global variable ‘Median_logR’
correctIntegerCN: no visible binding for global variable ‘Chr’
correctIntegerCN: no visible binding for global variable ‘LogRatio’
correctIntegerCN: no visible binding for global variable
‘Corrected_Copy_Number’
correctIntegerCN: no visible binding for global variable
‘Corrected_Call’
correctIntegerCN: no visible binding for global variable ‘TITAN_call’
correctIntegerCN: no visible binding for global variable ‘CopyNumber’
correctIntegerCN: no visible binding for global variable ‘TITANcall’
correctReadDepth: no visible global function definition for ‘queryHits’
correctReadcount: no visible global function definition for ‘loess’
correctReadcount: no visible global function definition for ‘predict’
correctReadcount: no visible global function definition for ‘approxfun’
correctReadcount: no visible global function definition for ‘lowess’
extendSegments: no visible binding for global variable ‘Start’
extendSegments: no visible binding for global variable ‘End’
extendSegments: no visible binding for global variable ‘Chromosome’
extendSegments: no visible binding for global variable ‘Start.snp’
extendSegments: no visible binding for global variable ‘End.snp’
extendSegments: no visible binding for global variable ‘Start.telo’
extendSegments: no visible binding for global variable ‘seq.info’
extractAlleleReadCounts: no visible global function definition for
‘xtabs’
extractAlleleReadCounts: no visible global function definition for
‘write.table’
getHaplotypesFromVCF: no visible global function definition for
‘rowRanges<-’
getHaplotypesFromVCF: no visible global function definition for
‘rowRanges’
getHaplotypesFromVCF: no visible global function definition for
‘na.omit’
getHaplotypesFromVCF: no visible global function definition for
‘unstrsplit’
getHaplotypesFromVCF: no visible global function definition for
‘queryHits’
getHaplotypesFromVCF: no visible global function definition for
‘DataFrame’
getOverlap: no visible global function definition for ‘as’
getOverlap: no visible global function definition for ‘queryHits’
getOverlap: no visible global function definition for ‘subjectHits’
getPositionOverlap: no visible global function definition for ‘as’
getSubcloneProfiles: no visible global function definition for
‘read.delim’
getSubcloneProfiles: no visible binding for global variable
‘CopyNumber’
getSubcloneProfiles: no visible binding for global variable ‘TITANcall’
loadAlleleCounts: no visible global function definition for
‘read.delim’
loadBXcountsFromBEDDir: no visible binding for global variable
‘BXcounts’
loadBXcountsFromBEDDir: no visible binding for global variable ‘BX’
loadBXcountsFromBEDDir: no visible global function definition for
‘keepChr’
loadHaplotypeAlleleCounts: no visible global function definition for
‘read.delim’
loadHaplotypeAlleleCounts: no visible global function definition for
‘subjectHits’
loadHaplotypeAlleleCounts: no visible global function definition for
‘as’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘phasedAlleleFraction’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘phasedCount’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘depth’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘SNPs’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘HaplotypeFraction’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘HaplotypeDepth.sum’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘HaplotypeBinDepth.sum’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘HaplotypeDepth.mean’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘HaplotypeBinDepth.mean’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘phaseSet’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘haplotypeBin’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘HaplotypeFraction.symmetric’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘HaplotypeDepth.sum.symmetric’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘HaplotypeDepth.mean.symmetric’
loadHaplotypeAlleleCounts: no visible global function definition for
‘.’
loadHaplotypeAlleleCounts: no visible global function definition for
‘na.omit’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘phasedCount.haploSymmetric’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘nonRef’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘phaseSet.aggr’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘HaplotypeRatio’
loadHaplotypeAlleleCounts: no visible binding for global variable
‘tumDepth’
loadReadCountsFromBed: no visible global function definition for
‘keepChr’
loadReadCountsFromBed: no visible global function definition for
‘excludeCentromere’
loadReadCountsFromBed: no visible global function definition for
‘filterByTargetedSequences’
mergeSegsByCol: no visible binding for global variable ‘Median_Ratio’
mergeSegsByCol: no visible binding for global variable ‘Median_logR’
mergeSegsByCol: no visible binding for global variable ‘End’
mergeSegsByCol: no visible binding for global variable ‘Length.snp.’
outlierObslik: no visible global function definition for ‘dunif’
outputModelParameters: no visible global function definition for
‘write.table’
outputTitanResults: no visible global function definition for
‘write.table’
outputTitanSegments: no visible binding for global variable ‘Sample’
plotAllelicCN: no visible binding for global variable ‘Allele.1’
plotAllelicCN: no visible binding for global variable ‘LogRatio’
plotAllelicCN: no visible binding for global variable ‘Allele.2’
plotAllelicCN: no visible binding for global variable ‘Chr’
plotAllelicCN: no visible binding for global variable ‘TITANcall’
plotAllelicCN: no visible global function definition for ‘par’
plotAllelicCN: no visible global function definition for ‘plot’
plotAllelicCN: no visible binding for global variable ‘CopyNumber’
plotAllelicCN: no visible global function definition for ‘points’
plotAllelicCN: no visible global function definition for ‘lines’
plotAllelicRatio: no visible binding for global variable ‘Chr’
plotAllelicRatio: no visible binding for global variable ‘TITANcall’
plotAllelicRatio: no visible global function definition for ‘par’
plotAllelicRatio: no visible global function definition for ‘plot’
plotAllelicRatio: no visible binding for global variable ‘AllelicRatio’
plotAllelicRatio: no visible global function definition for ‘lines’
plotCNlogRByChr: no visible binding for global variable ‘LogRatio’
plotCNlogRByChr: no visible binding for global variable ‘Median_logR’
plotCNlogRByChr: no visible binding for global variable ‘Chr’
plotCNlogRByChr: no visible binding for global variable ‘TITANcall’
plotCNlogRByChr: no visible global function definition for ‘par’
plotCNlogRByChr: no visible global function definition for ‘plot’
plotCNlogRByChr: no visible binding for global variable ‘CopyNumber’
plotCNlogRByChr: no visible global function definition for ‘lines’
plotCNlogRByChr: no visible binding for global variable ‘Chromosome’
plotCNlogRByChr : <anonymous>: no visible global function definition
for ‘lines’
plotCNlogRByChr: no visible binding for global variable
‘End_Position.bp.’
plotCNlogRByChr: no visible binding for global variable
‘Start_Position.bp.’
plotCNlogRByChr: no visible binding for global variable ‘Copy_Number’
plotChrLines: no visible global function definition for ‘lines’
plotChrLines: no visible global function definition for ‘axis’
plotClonalFrequency: no visible binding for global variable
‘ClonalCluster’
plotClonalFrequency: no visible binding for global variable
‘CellularPrevalence’
plotClonalFrequency: no visible binding for global variable ‘TITANcall’
plotClonalFrequency: no visible binding for global variable ‘Chr’
plotClonalFrequency: no visible global function definition for ‘par’
plotClonalFrequency: no visible global function definition for ‘plot’
plotClonalFrequency: no visible global function definition for ‘lines’
plotClonalFrequency: no visible global function definition for ‘mtext’
plotGeneAnnotation: no visible global function definition for ‘abline’
plotGeneAnnotation: no visible global function definition for ‘mtext’
plotHaplotypeFraction: no visible binding for global variable
‘HaplotypeRatio.1’
plotHaplotypeFraction: no visible binding for global variable
‘HaplotypeRatio’
plotHaplotypeFraction: no visible binding for global variable
‘HaplotypeRatio.2’
plotHaplotypeFraction: no visible binding for global variable ‘Chr’
plotHaplotypeFraction: no visible global function definition for ‘par’
plotHaplotypeFraction: no visible global function definition for ‘plot’
plotHaplotypeFraction: no visible global function definition for
‘points’
plotHaplotypeFraction: no visible binding for global variable
‘AllelicRatio’
plotHaplotypeFraction: no visible global function definition for
‘lines’
plotHaplotypeFraction: no visible binding for global variable
‘TITANcall’
plotSegmentMedians: no visible binding for global variable ‘Chromosome’
plotSegmentMedians: no visible binding for global variable ‘TITAN_call’
plotSegmentMedians: no visible global function definition for ‘par’
plotSegmentMedians: no visible binding for global variable
‘End_Position.bp.’
plotSegmentMedians: no visible global function definition for ‘.’
plotSegmentMedians: no visible binding for global variable
‘Start_Position.bp.’
plotSegmentMedians: no visible binding for global variable ‘MajorCN’
plotSegmentMedians: no visible binding for global variable ‘MinorCN’
plotSegmentMedians: no visible binding for global variable
‘Copy_Number’
plotSegmentMedians: no visible global function definition for ‘plot’
plotSegmentMedians : <anonymous>: no visible global function definition
for ‘lines’
plotSegmentMedians: no visible global function definition for ‘lines’
plotSubcloneProfiles: no visible binding for global variable ‘Chr’
plotSubcloneProfiles: no visible global function definition for ‘par’
plotSubcloneProfiles: no visible binding for global variable
‘CopyNumber’
plotSubcloneProfiles: no visible global function definition for ‘plot’
plotSubcloneProfiles: no visible global function definition for ‘axis’
plotSubcloneProfiles: no visible global function definition for
‘points’
plotSubcloneProfiles: no visible global function definition for ‘mtext’
plotSubcloneProfiles: no visible global function definition for ‘lines’
printSDbw: no visible global function definition for ‘write.table’
removeCentromereSegs: no visible binding for global variable
‘Chromosome’
removeCentromereSegs: no visible binding for global variable ‘Start’
removeCentromereSegs: no visible binding for global variable ‘End’
removeEmptyClusters: no visible global function definition for ‘tail’
runEMclonalCN: no visible binding for global variable ‘head’
updateParameters: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
. Allele.1 Allele.2 AllelicRatio BX BXcounts CellularPrevalence Chr
Chromosome ClonalCluster CopyNumber Copy_Number Corrected_Call
Corrected_Copy_Number DataFrame End End.snp End_Position.bp.
HaplotypeBinDepth.mean HaplotypeBinDepth.sum HaplotypeDepth.mean
HaplotypeDepth.mean.symmetric HaplotypeDepth.sum
HaplotypeDepth.sum.symmetric HaplotypeFraction
HaplotypeFraction.symmetric HaplotypeRatio HaplotypeRatio.1
HaplotypeRatio.2 Length.snp. LogRatio MajorCN Median_Ratio
Median_logR MinorCN SNPs Sample Start Start.snp Start.telo
Start_Position.bp. TITAN_call TITANcall TITANstate abline approxfun
as axis depth dunif excludeCentromere filterByTargetedSequences
haplotypeBin head keepChr lines loess logR_Copy_Number lowess mtext
na.omit nonRef par phaseSet phaseSet.aggr phasedAlleleFraction
phasedCount phasedCount.haploSymmetric plot points predict queryHits
read.delim rowRanges rowRanges<- seq.info subjectHits tail tumDepth
uniroot unstrsplit write.table xtabs
Consider adding
importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
"plot", "points")
importFrom("methods", "as")
importFrom("stats", "approxfun", "dunif", "loess", "lowess", "na.omit",
"predict", "uniroot", "xtabs")
importFrom("utils", "head", "read.delim", "tail", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘list’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
TitanCNA-package 25.745 0.482 26.456
runEMclonalCN 17.340 0.465 18.088
filterData 9.184 0.347 9.689
getPositionOverlap 8.797 0.349 9.249
correctReadDepth 8.501 0.352 8.972
* 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, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/TitanCNA.Rcheck/00check.log’
for details.
TitanCNA.Rcheck/00install.out
* installing *source* package ‘TitanCNA’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
fwd_backC_clonalCN.c:257:21: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((iZS==jZS)){
˜˜˜^˜˜˜˜
fwd_backC_clonalCN.c:257:21: note: remove extraneous parentheses around the comparison to silence this warning
if ((iZS==jZS)){
˜ ^ ˜
fwd_backC_clonalCN.c:257:21: note: use '=' to turn this equality comparison into an assignment
if ((iZS==jZS)){
^˜
=
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c getPositionOverlapC.c -o getPositionOverlapC.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c register.c -o register.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o TitanCNA.so fwd_backC_clonalCN.o getPositionOverlapC.o register.o viterbiC_clonalCN.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/TitanCNA.Rcheck/TitanCNA/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::slice’ by ‘dplyr::slice’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomeInfoDb::intersect’ by ‘dplyr::intersect’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::desc’ by ‘dplyr::desc’ when loading ‘TitanCNA’
Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::slice’ by ‘dplyr::slice’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomeInfoDb::intersect’ by ‘dplyr::intersect’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::desc’ by ‘dplyr::desc’ when loading ‘TitanCNA’
Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’
* DONE (TitanCNA)
TitanCNA.Rcheck/TitanCNA-Ex.timings
| name | user | system | elapsed | |
| TitanCNA-output | 1.790 | 0.042 | 1.847 | |
| TitanCNA-package | 25.745 | 0.482 | 26.456 | |
| TitanCNA-plotting | 4.660 | 0.065 | 4.624 | |
| computeSDbwIndex | 3.731 | 0.046 | 3.823 | |
| correctReadDepth | 8.501 | 0.352 | 8.972 | |
| extractAlleleReadCounts | 0.001 | 0.000 | 0.001 | |
| filterData | 9.184 | 0.347 | 9.689 | |
| getPositionOverlap | 8.797 | 0.349 | 9.249 | |
| haplotype | 0.001 | 0.000 | 0.001 | |
| loadAlleleCounts | 0.552 | 0.019 | 0.576 | |
| loadDefaultParameters | 0.093 | 0.002 | 0.098 | |
| runEMclonalCN | 17.340 | 0.465 | 18.088 | |
| viterbiClonalCN | 0.406 | 0.005 | 0.418 | |
| wigToRangedData | 0.463 | 0.027 | 0.499 | |