Gavin Ha
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/TitanCNA |
| Branch: RELEASE_3_10 |
| Last Commit: 7fad13c |
| Last Changed Date: 2019-10-29 13:08:56 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:40:00 -0400 (Wed, 15 Apr 2020).
| Package 1728/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TitanCNA 1.24.0 Gavin Ha
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: TitanCNA |
| Version: 1.24.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TitanCNA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TitanCNA_1.24.0.tar.gz |
| StartedAt: 2020-04-15 06:09:41 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:16:09 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 388.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TitanCNA.Rcheck |
| Warnings: 2 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TitanCNA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TitanCNA_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/TitanCNA.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.24.0’
* 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 ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::slice’ by ‘dplyr::slice’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomeInfoDb::intersect’ by ‘dplyr::intersect’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::desc’ by ‘dplyr::desc’ when loading ‘TitanCNA’
Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/TitanCNA.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 7.1Mb
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 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
‘ClonalCluster’
correctIntegerCN: no visible binding for global variable
‘Median_HaplotypeRatio’
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
‘Cellular_Prevalence’
correctIntegerCN: no visible binding for global variable ‘Chr’
correctIntegerCN: no visible binding for global variable ‘LogRatio’
correctIntegerCN: no visible binding for global variable
‘CellularPrevalence’
correctIntegerCN: no visible binding for global variable
‘Corrected_Ratio’
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
‘Corrected_MajorCN’
correctIntegerCN: no visible binding for global variable ‘MajorCN’
correctIntegerCN: no visible binding for global variable
‘Corrected_MinorCN’
correctIntegerCN: no visible binding for global variable ‘MinorCN’
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
‘PileupParam’
extractAlleleReadCounts: no visible global function definition for
‘BcfFile’
extractAlleleReadCounts: no visible global function definition for
‘scanBcf’
extractAlleleReadCounts: no visible global function definition for
‘ScanBamParam’
extractAlleleReadCounts: no visible global function definition for
‘scanBamFlag’
extractAlleleReadCounts: no visible global function definition for
‘BamFile’
extractAlleleReadCounts: no visible global function definition for
‘pileup’
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’
keepChr: no visible global function definition for ‘as’
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’
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
‘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 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.’
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 binding for global variable
‘TITANcall’
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’
plotIdiogram.hg38: no visible global function definition for ‘par’
plotIdiogram.hg38: no visible binding for global variable ‘lsegments’
plotIdiogram.hg38: no visible binding for global variable ‘lpolygon’
plotIdiogram.hg38: no visible global function definition for ‘plot’
plotIdiogram.hg38: no visible global function definition for ‘axis’
plotIdiogram.hg38: no visible global function definition for ‘text’
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 global function definition for ‘plot’
plotSegmentMedians : <anonymous>: no visible global function definition
for ‘lines’
plotSegmentMedians: no visible global function definition for ‘lines’
plotSegmentMedians: no visible binding for global variable
‘Copy_Number’
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 BamFile BcfFile
CellularPrevalence Cellular_Prevalence Chr Chromosome ClonalCluster
CopyNumber Copy_Number Corrected_Call Corrected_Copy_Number
Corrected_MajorCN Corrected_MinorCN Corrected_Ratio 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_HaplotypeRatio
Median_Ratio Median_logR MinorCN PileupParam SNPs Sample ScanBamParam
Start Start.snp Start.telo Start_Position.bp. TITAN_call TITANcall
abline approxfun as axis depth dunif excludeCentromere
filterByTargetedSequences haplotypeBin head lines loess
logR_Copy_Number lowess lpolygon lsegments mtext na.omit nonRef par
phaseSet phaseSet.aggr phasedAlleleFraction phasedCount
phasedCount.haploSymmetric pileup plot points predict queryHits
read.delim rowRanges rowRanges<- scanBamFlag scanBcf seq.info
subjectHits tail text tumDepth uniroot unstrsplit write.table
Consider adding
importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
"plot", "points", "text")
importFrom("methods", "as")
importFrom("stats", "approxfun", "dunif", "loess", "lowess", "na.omit",
"predict", "uniroot")
importFrom("utils", "head", "read.delim", "tail", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: correctCN.Rd:51-53: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘list’
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘plotIdiogram.hg38’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
TitanCNA-package 35.748 8.596 30.345
runEMclonalCN 23.753 1.222 24.063
TitanCNA-plotting 11.642 6.593 6.546
getPositionOverlap 8.955 1.279 9.046
filterData 9.332 0.481 9.851
correctReadDepth 8.540 1.073 8.598
computeSDbwIndex 5.514 1.041 5.051
TitanCNA-output 3.575 2.622 2.112
correctCN 3.062 2.702 1.136
* 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: 2 WARNINGs, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/TitanCNA.Rcheck/00check.log’
for details.
TitanCNA.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TitanCNA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘TitanCNA’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c getPositionOverlapC.c -o getPositionOverlapC.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c register.c -o register.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-TitanCNA/00new/TitanCNA/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::slice’ by ‘dplyr::slice’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomeInfoDb::intersect’ by ‘dplyr::intersect’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::desc’ by ‘dplyr::desc’ when loading ‘TitanCNA’
Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ 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 from temporary location
Warning: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::slice’ by ‘dplyr::slice’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomeInfoDb::intersect’ by ‘dplyr::intersect’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::desc’ by ‘dplyr::desc’ when loading ‘TitanCNA’
Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::slice’ by ‘dplyr::slice’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomeInfoDb::intersect’ by ‘dplyr::intersect’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::desc’ by ‘dplyr::desc’ when loading ‘TitanCNA’
Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’
** testing if installed package keeps a record of temporary installation path
* DONE (TitanCNA)
TitanCNA.Rcheck/TitanCNA-Ex.timings
| name | user | system | elapsed | |
| TitanCNA-output | 3.575 | 2.622 | 2.112 | |
| TitanCNA-package | 35.748 | 8.596 | 30.345 | |
| TitanCNA-plotting | 11.642 | 6.593 | 6.546 | |
| computeSDbwIndex | 5.514 | 1.041 | 5.051 | |
| correctCN | 3.062 | 2.702 | 1.136 | |
| correctReadDepth | 8.540 | 1.073 | 8.598 | |
| filterData | 9.332 | 0.481 | 9.851 | |
| getPositionOverlap | 8.955 | 1.279 | 9.046 | |
| haplotype | 0 | 0 | 0 | |
| loadAlleleCounts | 1.125 | 0.042 | 1.178 | |
| loadDefaultParameters | 0.001 | 0.000 | 0.001 | |
| runEMclonalCN | 23.753 | 1.222 | 24.063 | |
| viterbiClonalCN | 0.496 | 0.008 | 0.504 | |
| wigImport | 0.398 | 0.033 | 0.435 | |